LOCUS CAKJZR010000000 1190 rc DNA linear INV 01-NOV-2021 DEFINITION Synanthedon vespiformis, whole genome shotgun sequencing project. ACCESSION CAKJZR000000000 VERSION CAKJZR000000000.1 DBLINK BioProject: PRJEB48302 BioSample: SAMEA7701494 KEYWORDS WGS. SOURCE Synanthedon vespiformis ORGANISM Synanthedon vespiformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sesioidea; Sesiidae; Sesiinae; Synanthedonini; Synanthedon. REFERENCE 1 (bases 1 to 1190) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Synanthedon vespiformis whole genome shotgun (WGS) project has the project accession CAKJZR000000000. This version of the project (01) has the accession number CAKJZR010000000, and consists of sequences CAKJZR010000001-CAKJZR010001190. The assembly ilSynVesp1.1 is based on 94x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 23 contains a possible heterozygous inversion 1.45-4.5Mb. We cannot be sure of the orientation of the chromosome between these coordinates. FEATURES Location/Qualifiers source 1..1190 /organism="Synanthedon vespiformis" /mol_type="genomic DNA" /db_xref="taxon:1660703" WGS CAKJZR010000001-CAKJZR010001190 // LOCUS CAKJUZ010000000 4465 rc DNA linear INV 21-OCT-2021 DEFINITION Criorhina berberina, whole genome shotgun sequencing project. ACCESSION CAKJUZ000000000 VERSION CAKJUZ000000000.1 DBLINK BioProject: PRJEB48174 BioSample: SAMEA7701563 Sequence Read Archive: ERR6363267, ERR6363268, ERR6363269, ERR6363270, ERR6363271, ERR6436386 KEYWORDS WGS. SOURCE Criorhina berberina ORGANISM Criorhina berberina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Xylotini; Criorhina. REFERENCE 1 (bases 1 to 4465) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Criorhina berberina whole genome shotgun (WGS) project has the project accession CAKJUZ000000000. This version of the project (01) has the accession number CAKJUZ010000000, and consists of sequences CAKJUZ010000001-CAKJUZ010004465. The assembly idCriBerb1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Heterozygous inversion at Chromosome 1 - 38.53 - 44.62Mbp. FEATURES Location/Qualifiers source 1..4465 /organism="Criorhina berberina" /mol_type="genomic DNA" /db_xref="taxon:2663927" WGS CAKJUZ010000001-CAKJUZ010004465 // LOCUS CAKJUW010000000 771 rc DNA linear INV 21-OCT-2021 DEFINITION Limnephilus marmoratus, whole genome shotgun sequencing project. ACCESSION CAKJUW000000000 VERSION CAKJUW000000000.1 DBLINK BioProject: PRJEB48178 BioSample: SAMEA7520990 Sequence Read Archive: ERR6688485, ERR6688486, ERR6688487, ERR6688488, ERR6688489, ERR6688490, ERR6688491, ERR6688492, ERR6688493, ERR6688494, ERR6807999, ERR6939236 KEYWORDS WGS. SOURCE Limnephilus marmoratus ORGANISM Limnephilus marmoratus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Trichoptera; Integripalpia; Plenitentoria; Limnephiloidea; Limnephilidae; Limnephilinae; Limnephilini; Limnephilus. REFERENCE 1 (bases 1 to 771) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Limnephilus marmoratus whole genome shotgun (WGS) project has the project accession CAKJUW000000000. This version of the project (01) has the accession number CAKJUW010000000, and consists of sequences CAKJUW010000001-CAKJUW010000771. The assembly iiLimMarm1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 and 8 have a high level of shared Hi-C signal which seems likely to result from a high proportion of shared repeat. FEATURES Location/Qualifiers source 1..771 /organism="Limnephilus marmoratus" /mol_type="genomic DNA" /db_xref="taxon:1271730" WGS CAKJUW010000001-CAKJUW010000771 // LOCUS CAKJUV010000000 1250 rc DNA linear INV 21-OCT-2021 DEFINITION Selenia dentaria, whole genome shotgun sequencing project. ACCESSION CAKJUV000000000 VERSION CAKJUV000000000.1 DBLINK BioProject: PRJEB48176 BioSample: SAMEA7701559 Sequence Read Archive: ERR6688610, ERR6688611, ERR6688612, ERR6688613, ERR6688614, ERR6939252, ERR6939253 KEYWORDS WGS. SOURCE Selenia dentaria ORGANISM Selenia dentaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Selenia. REFERENCE 1 (bases 1 to 1250) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Selenia dentaria whole genome shotgun (WGS) project has the project accession CAKJUV000000000. This version of the project (01) has the accession number CAKJUV010000000, and consists of sequences CAKJUV010000001-CAKJUV010001250. The assembly ilSelDent1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1250 /organism="Selenia dentaria" /mol_type="genomic DNA" /db_xref="taxon:934894" WGS CAKJUV010000001-CAKJUV010001250 // LOCUS CAKJUN010000000 37 rc DNA linear INV 21-OCT-2021 DEFINITION Limnephilus marmoratus, whole genome shotgun sequencing project. ACCESSION CAKJUN000000000 VERSION CAKJUN000000000.1 DBLINK BioProject: PRJEB48179 BioSample: SAMEA7520990 Sequence Read Archive: ERR6688485, ERR6688486, ERR6688487, ERR6688488, ERR6688489, ERR6688490, ERR6688491, ERR6688492, ERR6688493, ERR6688494, ERR6807999, ERR6939236 KEYWORDS WGS. SOURCE Limnephilus marmoratus ORGANISM Limnephilus marmoratus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Trichoptera; Integripalpia; Plenitentoria; Limnephiloidea; Limnephilidae; Limnephilinae; Limnephilini; Limnephilus. REFERENCE 1 (bases 1 to 37) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Limnephilus marmoratus whole genome shotgun (WGS) project has the project accession CAKJUN000000000. This version of the project (01) has the accession number CAKJUN010000000, and consists of sequences CAKJUN010000001-CAKJUN010000037. The assembly iiLimMarm1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 and 8 have a high level of shared Hi-C signal which seems likely to result from a high proportion of shared repeat. FEATURES Location/Qualifiers source 1..37 /organism="Limnephilus marmoratus" /mol_type="genomic DNA" /db_xref="taxon:1271730" WGS CAKJUN010000001-CAKJUN010000037 // LOCUS CAKJUM010000000 37 rc DNA linear INV 21-OCT-2021 DEFINITION Selenia dentaria, whole genome shotgun sequencing project. ACCESSION CAKJUM000000000 VERSION CAKJUM000000000.1 DBLINK BioProject: PRJEB48177 BioSample: SAMEA7701559 Sequence Read Archive: ERR6688610, ERR6688611, ERR6688612, ERR6688613, ERR6688614, ERR6939252, ERR6939253 KEYWORDS WGS. SOURCE Selenia dentaria ORGANISM Selenia dentaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Selenia. REFERENCE 1 (bases 1 to 37) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Selenia dentaria whole genome shotgun (WGS) project has the project accession CAKJUM000000000. This version of the project (01) has the accession number CAKJUM010000000, and consists of sequences CAKJUM010000001-CAKJUM010000037. The assembly ilSelDent1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..37 /organism="Selenia dentaria" /mol_type="genomic DNA" /db_xref="taxon:934894" WGS CAKJUM010000001-CAKJUM010000037 // LOCUS CAKJUL010000000 23 rc DNA linear INV 21-OCT-2021 DEFINITION Criorhina berberina, whole genome shotgun sequencing project. ACCESSION CAKJUL000000000 VERSION CAKJUL000000000.1 DBLINK BioProject: PRJEB48175 BioSample: SAMEA7701563 Sequence Read Archive: ERR6363267, ERR6363268, ERR6363269, ERR6363270, ERR6363271, ERR6436386 KEYWORDS WGS. SOURCE Criorhina berberina ORGANISM Criorhina berberina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Xylotini; Criorhina. REFERENCE 1 (bases 1 to 23) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (18-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Criorhina berberina whole genome shotgun (WGS) project has the project accession CAKJUL000000000. This version of the project (01) has the accession number CAKJUL010000000, and consists of sequences CAKJUL010000001-CAKJUL010000023. The assembly idCriBerb1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Heterozygous inversion at Chromosome 1 - 38.53 - 44.62Mbp. FEATURES Location/Qualifiers source 1..23 /organism="Criorhina berberina" /mol_type="genomic DNA" /db_xref="taxon:2663927" WGS CAKJUL010000001-CAKJUL010000023 // LOCUS CAJUYF020000000 2165 rc DNA linear VRT 01-NOV-2021 DEFINITION Pholis gunnellus, whole genome shotgun sequencing project. ACCESSION CAJUYF000000000 VERSION CAJUYF000000000.2 DBLINK BioProject: PRJEB45448 BioSample: SAMEA7522838 KEYWORDS WGS. SOURCE Pholis gunnellus (rock gunnel) ORGANISM Pholis gunnellus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Perciformes; Cottioidei; Zoarcales; Pholidae; Pholis. REFERENCE 1 (bases 1 to 2165) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 2165) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJUYF000000000.1. The Pholis gunnellus whole genome shotgun (WGS) project has the project accession CAJUYF000000000. This version of the project (02) has the accession number CAJUYF020000000, and consists of sequences CAJUYF020000001-CAJUYF020002165. The assembly fPhoGun1.2 is based on 45x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2165 /organism="Pholis gunnellus" /mol_type="genomic DNA" /db_xref="taxon:56726" WGS CAJUYF020000001-CAJUYF020002165 // LOCUS CAJUXR020000000 76 rc DNA linear VRT 01-NOV-2021 DEFINITION Pholis gunnellus, whole genome shotgun sequencing project. ACCESSION CAJUXR000000000 VERSION CAJUXR000000000.2 DBLINK BioProject: PRJEB45449 BioSample: SAMEA7522838 KEYWORDS WGS. SOURCE Pholis gunnellus (rock gunnel) ORGANISM Pholis gunnellus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Perciformes; Cottioidei; Zoarcales; Pholidae; Pholis. REFERENCE 1 (bases 1 to 76) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 76) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJUXR000000000.1. The Pholis gunnellus whole genome shotgun (WGS) project has the project accession CAJUXR000000000. This version of the project (02) has the accession number CAJUXR020000000, and consists of sequences CAJUXR020000001-CAJUXR020000076. The assembly fPhoGun1.2 is based on 45x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..76 /organism="Pholis gunnellus" /mol_type="genomic DNA" /db_xref="taxon:56726" WGS CAJUXR020000001-CAJUXR020000076 // LOCUS CAJRBF020000000 24 rc DNA linear INV 01-NOV-2021 DEFINITION Zygaena filipendulae, whole genome shotgun sequencing project. ACCESSION CAJRBF000000000 VERSION CAJRBF000000000.2 DBLINK BioProject: PRJEB44634 BioSample: SAMEA7519846 KEYWORDS WGS. SOURCE Zygaena filipendulae ORGANISM Zygaena filipendulae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Zygaenoidea; Zygaenidae; Zygaeninae; Zygaena. REFERENCE 1 (bases 1 to 24) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 24) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJRBF000000000.1. The Zygaena filipendulae whole genome shotgun (WGS) project has the project accession CAJRBF000000000. This version of the project (02) has the accession number CAJRBF020000000, and consists of sequences CAJRBF020000001-CAJRBF020000024. The assembly ilZygFili1.2 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..24 /organism="Zygaena filipendulae" /mol_type="genomic DNA" /db_xref="taxon:287375" WGS CAJRBF020000001-CAJRBF020000024 // LOCUS CAJRBE020000000 417 rc DNA linear INV 01-NOV-2021 DEFINITION Zygaena filipendulae, whole genome shotgun sequencing project. ACCESSION CAJRBE000000000 VERSION CAJRBE000000000.2 DBLINK BioProject: PRJEB44635 BioSample: SAMEA7519846 KEYWORDS WGS. SOURCE Zygaena filipendulae ORGANISM Zygaena filipendulae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Zygaenoidea; Zygaenidae; Zygaeninae; Zygaena. REFERENCE 1 (bases 1 to 417) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 417) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJRBE000000000.1. The Zygaena filipendulae whole genome shotgun (WGS) project has the project accession CAJRBE000000000. This version of the project (02) has the accession number CAJRBE020000000, and consists of sequences CAJRBE020000001-CAJRBE020000417. The assembly ilZygFili1.2 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..417 /organism="Zygaena filipendulae" /mol_type="genomic DNA" /db_xref="taxon:287375" WGS CAJRBE020000001-CAJRBE020000417 // LOCUS CAJQFL020000000 20 rc DNA linear INV 01-NOV-2021 DEFINITION Hedya salicella, whole genome shotgun sequencing project. ACCESSION CAJQFL000000000 VERSION CAJQFL000000000.2 DBLINK BioProject: PRJEB43994 BioSample: SAMEA7520688 KEYWORDS WGS. SOURCE Hedya salicella ORGANISM Hedya salicella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Olethreutini; Hedya. REFERENCE 1 (bases 1 to 20) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 20) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJQFL000000000.1. The Hedya salicella whole genome shotgun (WGS) project has the project accession CAJQFL000000000. This version of the project (02) has the accession number CAJQFL020000000, and consists of sequences CAJQFL020000001-CAJQFL020000020. The assembly ilHedSali1.2 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..20 /organism="Hedya salicella" /mol_type="genomic DNA" /db_xref="taxon:1869985" WGS CAJQFL020000001-CAJQFL020000020 // LOCUS CAJQFJ020000000 1461 rc DNA linear INV 01-NOV-2021 DEFINITION Hedya salicella, whole genome shotgun sequencing project. ACCESSION CAJQFJ000000000 VERSION CAJQFJ000000000.2 DBLINK BioProject: PRJEB43995 BioSample: SAMEA7520688 KEYWORDS WGS. SOURCE Hedya salicella ORGANISM Hedya salicella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Olethreutini; Hedya. REFERENCE 1 (bases 1 to 1461) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 1461) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT On Nov 18, 2021 this sequence version replaced CAJQFJ000000000.1. The Hedya salicella whole genome shotgun (WGS) project has the project accession CAJQFJ000000000. This version of the project (02) has the accession number CAJQFJ020000000, and consists of sequences CAJQFJ020000001-CAJQFJ020001461. The assembly ilHedSali1.2 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1461 /organism="Hedya salicella" /mol_type="genomic DNA" /db_xref="taxon:1869985" WGS CAJQFJ020000001-CAJQFJ020001461 // LOCUS CAKAOP010000000 1259 rc DNA linear INV 19-OCT-2021 DEFINITION Agrochola macilenta, whole genome shotgun sequencing project. ACCESSION CAKAOP000000000 VERSION CAKAOP000000000.1 DBLINK BioProject: PRJEB47750 BioSample: SAMEA8603207 KEYWORDS WGS. SOURCE Agrochola macilenta ORGANISM Agrochola macilenta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Agrochola. REFERENCE 1 (bases 1 to 1259) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Agrochola macilenta whole genome shotgun (WGS) project has the project accession CAKAOP000000000. This version of the project (01) has the accession number CAKAOP010000000, and consists of sequences CAKAOP010000001-CAKAOP010001259. The assembly ilAgrMaci1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1259 /organism="Agrochola macilenta" /mol_type="genomic DNA" /db_xref="taxon:987872" WGS CAKAOP010000001-CAKAOP010001259 // LOCUS CAKAOO010000000 3 rc DNA linear INV 19-OCT-2021 DEFINITION Agrochola macilenta, whole genome shotgun sequencing project. ACCESSION CAKAOO000000000 VERSION CAKAOO000000000.1 DBLINK BioProject: PRJEB47751 BioSample: SAMEA8603207 KEYWORDS WGS. SOURCE Agrochola macilenta ORGANISM Agrochola macilenta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Agrochola. REFERENCE 1 (bases 1 to 3) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Agrochola macilenta whole genome shotgun (WGS) project has the project accession CAKAOO000000000. This version of the project (01) has the accession number CAKAOO010000000, and consists of sequences CAKAOO010000001-CAKAOO010000003. The assembly ilAgrMaci1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3 /organism="Agrochola macilenta" /mol_type="genomic DNA" /db_xref="taxon:987872" WGS CAKAOO010000001-CAKAOO010000003 // LOCUS JAJIAZ010000000 1199 rc DNA linear MAM 10-NOV-2021 DEFINITION Diceros bicornis minor isolate mBicDic1, whole genome shotgun sequencing project. ACCESSION JAJIAZ000000000 VERSION JAJIAZ000000000.1 DBLINK BioProject: PRJNA773943 BioSample: SAMN22047685 KEYWORDS WGS. SOURCE Diceros bicornis minor ORGANISM Diceros bicornis minor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Perissodactyla; Rhinocerotidae; Diceros. REFERENCE 1 (bases 1 to 1199) AUTHORS Koepfli,K.-P., Pukazhenthi,B., Formenti,G., Balacco,J., Mountcastle,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Diceros bicornis minor (Southern black rhinoceros), mBicDic1, paternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1199) AUTHORS Koepfli,K.-P., Pukazhenthi,B., Formenti,G., Balacco,J., Mountcastle,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (30-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Diceros bicornis minor whole genome shotgun (WGS) project has the project accession JAJIAZ000000000. This version of the project (01) has the accession number JAJIAZ010000000, and consists of sequences JAJIAZ010000001-JAJIAZ010001199. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: Trio HiFiasm v. 0.15.1-r329; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.2 Assembly Name :: mDicBic1.pat.decon Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 30.57x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1199 /organism="Diceros bicornis minor" /mol_type="genomic DNA" /isolate="mBicDic1" /sub_species="minor" /db_xref="taxon:77932" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="USA" /lat_lon="32.1795 N 97.7972 W" /collected_by="Budhan Pukazhenthi" WGS JAJIAZ010000001-JAJIAZ010001199 // LOCUS JAJIAY010000000 1075 rc DNA linear MAM 10-NOV-2021 DEFINITION Diceros bicornis minor isolate mBicDic1, whole genome shotgun sequencing project. ACCESSION JAJIAY000000000 VERSION JAJIAY000000000.1 DBLINK BioProject: PRJNA773944 BioSample: SAMN22047685 KEYWORDS WGS. SOURCE Diceros bicornis minor ORGANISM Diceros bicornis minor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Perissodactyla; Rhinocerotidae; Diceros. REFERENCE 1 (bases 1 to 1075) AUTHORS Koepfli,K.-P., Pukazhenthi,B., Formenti,G., Balacco,J., Mountcastle,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Diceros bicornis minor (Southern black rhinoceros), mBicDic1, maternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1075) AUTHORS Koepfli,K.-P., Pukazhenthi,B., Formenti,G., Balacco,J., Mountcastle,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (30-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Diceros bicornis minor whole genome shotgun (WGS) project has the project accession JAJIAY000000000. This version of the project (01) has the accession number JAJIAY010000000, and consists of sequences JAJIAY010000001-JAJIAY010001075. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: Trio HiFiasm v. 0.15.1-r329; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.2 Assembly Name :: mDicBic1.mat.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 30.57x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1075 /organism="Diceros bicornis minor" /mol_type="genomic DNA" /isolate="mBicDic1" /sub_species="minor" /db_xref="taxon:77932" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="USA" /lat_lon="32.1795 N 97.7972 W" /collected_by="Budhan Pukazhenthi" WGS JAJIAY010000001-JAJIAY010001075 WGS_SCAFLD CM036946-CM036987 // LOCUS JAJHSZ010000000 178 rc DNA linear VRT 08-NOV-2021 DEFINITION Porphyrio hochstetteri isolate bPorHoc1, whole genome shotgun sequencing project. ACCESSION JAJHSZ000000000 VERSION JAJHSZ000000000.1 DBLINK BioProject: PRJNA774332 BioSample: SAMN22550412 KEYWORDS WGS. SOURCE Porphyrio hochstetteri (South Island takahe) ORGANISM Porphyrio hochstetteri Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Gruiformes; Rallidae; Porphyrio. REFERENCE 1 (bases 1 to 178) AUTHORS Urban,L., Digby,A., Eason,D., Vercoe,D., Gemmell,N., Formenti,G., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Takahe Recovery Program,P. TITLE Porphyrio hochstetteri (takahe) genome, bPorHoc1, paternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 178) AUTHORS Urban,L., Digby,A., Eason,D., Vercoe,D., Gemmell,N., Formenti,G., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Takahe Recovery Program,P. TITLE Direct Submission JOURNAL Submitted (31-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Porphyrio hochstetteri whole genome shotgun (WGS) project has the project accession JAJHSZ000000000. This version of the project (01) has the accession number JAJHSZ010000000, and consists of sequences JAJHSZ010000001-JAJHSZ010000178. ##Genome-Assembly-Data-START## Assembly Date :: 20-JUL-2021 Assembly Method :: Trio HiFiasm v. 0.15.1-r329; purge_dups v. 1.2.5; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.3; gEVAL manual curation v. 2021-07-20; cutadapt (done in beginning) v. 3.2 Assembly Name :: bPorHoc1.pat.decon Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 36.82x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..178 /organism="Porphyrio hochstetteri" /mol_type="genomic DNA" /isolate="bPorHoc1" /db_xref="taxon:439704" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="New Zealand: Burwood" /lat_lon="43.499998 S 172.6999972 E" /collection_date="2020-02-13" /collected_by="Glen Greaves" WGS JAJHSZ010000001-JAJHSZ010000178 // LOCUS JAJHSY010000000 174 rc DNA linear VRT 08-NOV-2021 DEFINITION Porphyrio hochstetteri isolate bPorHoc1, whole genome shotgun sequencing project. ACCESSION JAJHSY000000000 VERSION JAJHSY000000000.1 DBLINK BioProject: PRJNA774331 BioSample: SAMN22550412 KEYWORDS WGS. SOURCE Porphyrio hochstetteri (South Island takahe) ORGANISM Porphyrio hochstetteri Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Gruiformes; Rallidae; Porphyrio. REFERENCE 1 (bases 1 to 174) AUTHORS Urban,L., Digby,A., Eason,D., Vercoe,D., Gemmell,N., Formenti,G., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Takahe Recovery Program,P. TITLE Porphyrio hochstetteri (takahe) genome, bPorHoc1, maternal + Z haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 174) AUTHORS Urban,L., Digby,A., Eason,D., Vercoe,D., Gemmell,N., Formenti,G., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Takahe Recovery Program,P. TITLE Direct Submission JOURNAL Submitted (06-NOV-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Porphyrio hochstetteri whole genome shotgun (WGS) project has the project accession JAJHSY000000000. This version of the project (01) has the accession number JAJHSY010000000, and consists of sequences JAJHSY010000001-JAJHSY010000174. ##Genome-Assembly-Data-START## Assembly Date :: 06-NOV-2021 Assembly Method :: Trio HiFiasm v. 0.15.1-r329; purge_dups v. 1.2.5; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.3; gEVAL manual curation v. 2021-07-20; VGP trio pipeline v. 2.0; cutadapt (done in beginning) v. 3.2; gEVAL manual curation v. 2021-11-06 Assembly Name :: bPorHoc1.mat.Z.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 36.82x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..174 /organism="Porphyrio hochstetteri" /mol_type="genomic DNA" /isolate="bPorHoc1" /db_xref="taxon:439704" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="New Zealand: Burwood" /lat_lon="43.499998 S 172.6999972 E" /collection_date="2020-02-13" /collected_by="Glen Greaves" WGS JAJHSY010000001-JAJHSY010000174 WGS_SCAFLD CM036905-CM036939 // LOCUS JAJGRZ010000000 4000 rc DNA linear VRT 05-NOV-2021 DEFINITION Hemiscyllium ocellatum isolate sHemOce1, whole genome shotgun sequencing project. ACCESSION JAJGRZ000000000 VERSION JAJGRZ000000000.1 DBLINK BioProject: PRJNA774309 BioSample: SAMN22550098 KEYWORDS WGS. SOURCE Hemiscyllium ocellatum (epaulette shark) ORGANISM Hemiscyllium ocellatum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Orectolobiformes; Hemiscylliidae; Hemiscyllium. REFERENCE 1 (bases 1 to 4000) AUTHORS Naylor,G., Burgess,S., Fedrigo,O., Schartl,M., Currie,P., Tulenko,F., Balacco,J., Mountcastle,J., Haase,B., Tracey,A., Sims,Y., Howe,K., Mullikin,J. and Jarvis,E.D. TITLE Hemiscyllium ocellatum (epaulette shark) genome, sHemOce1, maternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 4000) AUTHORS Naylor,G., Burgess,S., Fedrigo,O., Schartl,M., Currie,P., Tulenko,F., Balacco,J., Mountcastle,J., Haase,B., Tracey,A., Sims,Y., Howe,K., Mullikin,J. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (31-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Hemiscyllium ocellatum whole genome shotgun (WGS) project has the project accession JAJGRZ000000000. This version of the project (01) has the accession number JAJGRZ010000000, and consists of sequences JAJGRZ010000001-JAJGRZ010004000. ##Genome-Assembly-Data-START## Assembly Date :: 28-MAY-2021 Assembly Method :: TrioCanu v. 2.1; purge_dups v. 1.2.5; Scaff 10x v. 4.2; Bionano Solve v. 3.6.1_11162020; Salsa2 HiC v. 2.2; variantCaller v. 2.3.3; Longranger Align v. 2.2.2; Freebayes v. 1.3; gEVAL manual curation v. 2021-05-28; VGP pipeline v. 1.6 Assembly Name :: sHemOce1.mat.decon Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 148.57x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Bionano Genomics DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..4000 /organism="Hemiscyllium ocellatum" /mol_type="genomic DNA" /isolate="sHemOce1" /specimen_voucher="Juvenile #1654" /db_xref="taxon:170820" /sex="male" /tissue_type="spleen" /dev_stage="juvenile" /country="Australia: Clayton, Melbourne, Victoria" /lat_lon="37.9105 S 145.1293 E" /collection_date="2019-01-02" /collected_by="Frank Tulenko" WGS JAJGRZ010000001-JAJGRZ010004000 // LOCUS JAJGRY010000000 1963 rc DNA linear VRT 05-NOV-2021 DEFINITION Hemiscyllium ocellatum isolate sHemOce1, whole genome shotgun sequencing project. ACCESSION JAJGRY000000000 VERSION JAJGRY000000000.1 DBLINK BioProject: PRJNA774310 BioSample: SAMN22550098 KEYWORDS WGS. SOURCE Hemiscyllium ocellatum (epaulette shark) ORGANISM Hemiscyllium ocellatum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Orectolobiformes; Hemiscylliidae; Hemiscyllium. REFERENCE 1 (bases 1 to 1963) AUTHORS Naylor,G., Burgess,S., Fedrigo,O., Schartl,M., Currie,P., Tulenko,F., Balacco,J., Mountcastle,J., Haase,B., Tracey,A., Sims,Y., Howe,K., Mullikin,J. and Jarvis,E.D. TITLE Hemiscyllium ocellatum (epaulette shark) genome, sHemOce1, paternal + X haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1963) AUTHORS Naylor,G., Burgess,S., Fedrigo,O., Schartl,M., Currie,P., Tulenko,F., Balacco,J., Mountcastle,J., Haase,B., Tracey,A., Sims,Y., Howe,K., Mullikin,J. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (31-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Hemiscyllium ocellatum whole genome shotgun (WGS) project has the project accession JAJGRY000000000. This version of the project (01) has the accession number JAJGRY010000000, and consists of sequences JAJGRY010000001-JAJGRY010001963. ##Genome-Assembly-Data-START## Assembly Date :: 28-MAY-2021 Assembly Method :: TrioCanu v. 2.1; purge_dups v. 1.2.5; Scaff 10x v. 4.2; Bionano Solve v. 3.6.1_11162020; Salsa2 HiC v. 2.2; variantCaller v. 2.3.3; Longranger Align v. 2.2.2; Freebayes v. 1.3; gEVAL manual curation v. 2021-05-28; VGP Pipeline v. 1.6 Assembly Name :: sHemOce1.pat.X.cur. Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 148.57x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Bionano Genomics DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1963 /organism="Hemiscyllium ocellatum" /mol_type="genomic DNA" /isolate="sHemOce1" /specimen_voucher="Juvenile #1654" /db_xref="taxon:170820" /sex="male" /tissue_type="spleen" /dev_stage="juvenile" /country="Australia: Clayton, Melbourne, Victoria" /lat_lon="37.9105 S 145.1293 E" /collection_date="2019-01-02" /collected_by="Frank Tulenko" WGS JAJGRY010000001-JAJGRY010001963 WGS_SCAFLD CM036659-CM036712 WGS_SCAFLD CM036752 // LOCUS JAJGRG010000000 1476 rc DNA linear VRT 05-NOV-2021 DEFINITION Tautogolabrus adspersus isolate fTauAds1, whole genome shotgun sequencing project. ACCESSION JAJGRG000000000 VERSION JAJGRG000000000.1 DBLINK BioProject: PRJNA774879 BioSample: SAMN22589422 KEYWORDS WGS. SOURCE Tautogolabrus adspersus (cunner) ORGANISM Tautogolabrus adspersus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Labriformes; Labridae; Tautogolabrus. REFERENCE 1 (bases 1 to 1476) AUTHORS Eindfelt,T., Jue,N., Young,H., Formenti,G., Balacco,J., Mountcastle,J., Collins,J., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Tautogolabrus adspersus (cunner) genome, fTauAds1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1476) AUTHORS Eindfelt,T., Jue,N., Young,H., Formenti,G., Balacco,J., Mountcastle,J., Collins,J., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (31-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Tautogolabrus adspersus whole genome shotgun (WGS) project has the project accession JAJGRG000000000. This version of the project (01) has the accession number JAJGRG010000000, and consists of sequences JAJGRG010000001-JAJGRG010001476. ##Genome-Assembly-Data-START## Assembly Date :: 18-OCT-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. SMRTLink8, pbalign:0.3.2,; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano Solve DLS v. 3.4_06042019a; Arrow polishing and gap filling v. pbgcpp:1.9.0.1; Longranger Align v. 2.2.2; Deepvariant v. 1.1.0 Assembly Name :: fTauAds1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 103.79x Sequencing Technology :: PacBio Sequel II CLR; 10X Gemonics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1476 /organism="Tautogolabrus adspersus" /mol_type="genomic DNA" /isolate="fTauAds1" /db_xref="taxon:34787" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="Canada: Alderney Landing, Halifax" /lat_lon="44.66 N 63.57 W" /collection_date="2019-08-12" /collected_by="Tony Einfeldt" WGS JAJGRG010000001-JAJGRG010001476 // LOCUS JAJGRF010000000 64 rc DNA linear VRT 05-NOV-2021 DEFINITION Tautogolabrus adspersus isolate fTauAds1, whole genome shotgun sequencing project. ACCESSION JAJGRF000000000 VERSION JAJGRF000000000.1 DBLINK BioProject: PRJNA774878 BioSample: SAMN22589422 KEYWORDS WGS. SOURCE Tautogolabrus adspersus (cunner) ORGANISM Tautogolabrus adspersus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Labriformes; Labridae; Tautogolabrus. REFERENCE 1 (bases 1 to 64) AUTHORS Eindfelt,T., Jue,N., Young,H., Formenti,G., Balacco,J., Mountcastle,J., Collins,J., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Tautogolabrus adspersus (cunner) genome, fTauAds1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 64) AUTHORS Eindfelt,T., Jue,N., Young,H., Formenti,G., Balacco,J., Mountcastle,J., Collins,J., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (31-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Tautogolabrus adspersus whole genome shotgun (WGS) project has the project accession JAJGRF000000000. This version of the project (01) has the accession number JAJGRF010000000, and consists of sequences JAJGRF010000001-JAJGRF010000064. ##Genome-Assembly-Data-START## Assembly Date :: 18-OCT-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. SMRTLink8, pbalign:0.3.2,; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano Solve DLS v. 3.4_06042019a; Arrow polishing and gap filling v. pbgcpp:1.9.0.1; Longranger Align v. 2.2.2; Deepvariant v. 1.1.0 Assembly Name :: fTauAds1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 103.79x Sequencing Technology :: PacBio Sequel II CLR; 10X Gemonics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..64 /organism="Tautogolabrus adspersus" /mol_type="genomic DNA" /isolate="fTauAds1" /db_xref="taxon:34787" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="Canada: Alderney Landing, Halifax" /lat_lon="44.66 N 63.57 W" /collection_date="2019-08-12" /collected_by="Tony Einfeldt" WGS JAJGRF010000001-JAJGRF010000064 WGS_SCAFLD CM036534-CM036557 WGS_SCAFLD CM036584 // LOCUS JAJGSU010000000 1535 rc DNA linear VRT 05-NOV-2021 DEFINITION Trogon surrucura isolate bTroSur1, whole genome shotgun sequencing project. ACCESSION JAJGSU000000000 VERSION JAJGSU000000000.1 DBLINK BioProject: PRJNA774296 BioSample: SAMN22550082 KEYWORDS WGS. SOURCE Trogon surrucura (Suruca trogon) ORGANISM Trogon surrucura Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Trogoniformes; Trogonidae; Trogon. REFERENCE 1 (bases 1 to 1535) AUTHORS Gilbert,M.T.P., Banin,D.A., Mountcastle,J., Balacco,J.R., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K., Graves,G., Fedrigo,O. and Jarvis,E.D. TITLE Trogon surrucura (Surucua trogon) genome, bTroSur1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1535) AUTHORS Gilbert,M.T.P., Banin,D.A., Mountcastle,J., Balacco,J.R., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K., Graves,G., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Trogon surrucura whole genome shotgun (WGS) project has the project accession JAJGSU000000000. This version of the project (01) has the accession number JAJGSU010000000, and consists of sequences JAJGSU010000001-JAJGSU010001535. ##Genome-Assembly-Data-START## Assembly Date :: 25-MAY-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deep variant polishing v. 1.1.0; gEVAL manual curation v. 2021-09-24; VGP pipeline v. 1.7 Assembly Name :: bTroSur1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 78.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Bionano Genomics Saphyr DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1535 /organism="Trogon surrucura" /mol_type="genomic DNA" /isolate="bTroSur1" /specimen_voucher="USNM 620787" /bio_material="B05987" /db_xref="taxon:297711" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="adult" /country="Argentina: Posadas, Misiones" /lat_lon="26.955278 S 55.087778 W" /collection_date="1995-10-29" /collected_by="D. A. Banin" WGS JAJGSU010000001-JAJGSU010001535 // LOCUS JAJGQX010000000 2405 rc DNA linear VRT 05-NOV-2021 DEFINITION Hemiprocne comata isolate bHemCom1, whole genome shotgun sequencing project. ACCESSION JAJGQX000000000 VERSION JAJGQX000000000.1 DBLINK BioProject: PRJNA774830 BioSample: SAMN22588383 KEYWORDS WGS. SOURCE Hemiprocne comata ORGANISM Hemiprocne comata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Apodiformes; Apodidae; Hemiprocninae; Hemiprocne. REFERENCE 1 (bases 1 to 2405) AUTHORS Gilbert,M.T.P., Gaige,J., Mountcastle,J., Formenti,G., Phelan,S., Sims,Y., Ross,C., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Hemiprocne comata (whiskered treeswift) genome, bHemCom1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 2405) AUTHORS Gilbert,M.T.P., Gaige,J., Mountcastle,J., Formenti,G., Phelan,S., Sims,Y., Ross,C., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Hemiprocne comata whole genome shotgun (WGS) project has the project accession JAJGQX000000000. This version of the project (01) has the accession number JAJGQX010000000, and consists of sequences JAJGQX010000001-JAJGQX010002405. ##Genome-Assembly-Data-START## Assembly Date :: 24-SEP-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deep variant polishing v. 1.1.0; gEVAL manual curation v. 2021-09-24; VGP pipeline v. 1.7 Assembly Name :: bHemCom1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 80.12x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Bionano Genomics Saphyre DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2405 /organism="Hemiprocne comata" /mol_type="genomic DNA" /isolate="bHemCom1" /specimen_voucher="USNM 607338" /bio_material="B03790" /db_xref="taxon:243314" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="adult" /country="Philippines: Cagayan, Luzon Island (Barrio Via Sitio Hot Springs Baggao Mun.)" /lat_lon="17.85 N 121.98 E" /collection_date="1989-05-10" /collected_by="C. A. Ross" WGS JAJGQX010000001-JAJGQX010002405 // LOCUS JAJGSS010000000 749 rc DNA linear VRT 05-NOV-2021 DEFINITION Theristicus caerulescens isolate bTheCae1, whole genome shotgun sequencing project. ACCESSION JAJGSS000000000 VERSION JAJGSS000000000.1 DBLINK BioProject: PRJNA774321 BioSample: SAMN22550094 KEYWORDS WGS. SOURCE Theristicus caerulescens (plumbeous ibis) ORGANISM Theristicus caerulescens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Pelecaniformes; Threskiornithidae; Theristicus. REFERENCE 1 (bases 1 to 749) AUTHORS Gilbert,M.T.P., Milensky,C., Mountcastle,J., Balacco,J., Formenti,G., Pelan,S., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Theristicus caerulescens (plumbeous ibis) genome, bTheCae1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 749) AUTHORS Gilbert,M.T.P., Milensky,C., Mountcastle,J., Balacco,J., Formenti,G., Pelan,S., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Theristicus caerulescens whole genome shotgun (WGS) project has the project accession JAJGSS000000000. This version of the project (01) has the accession number JAJGSS010000000, and consists of sequences JAJGSS010000001-JAJGSS010000749. ##Genome-Assembly-Data-START## Assembly Date :: 25-MAY-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deep variant polishing v. 1.1.0; gEVAL manual curation v. 2021-05-25; VGP pipeline v. 1.7 Assembly Name :: bTheCae1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 123.5x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Bionano Genomics Saphyr DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..749 /organism="Theristicus caerulescens" /mol_type="genomic DNA" /isolate="bTheCae1" /specimen_voucher="USNM 636095" /bio_material="B20749" /db_xref="taxon:1118847" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="juvenile chick" /country="Uruguay: Rocha" /lat_lon="33.741944 S 53.746111 W" /collection_date="2005-10-26" /collected_by="C. M. Milensky" WGS JAJGSS010000001-JAJGSS010000749 // LOCUS JAJGST010000000 182 rc DNA linear VRT 05-NOV-2021 DEFINITION Trogon surrucura isolate bTroSur1, whole genome shotgun sequencing project. ACCESSION JAJGST000000000 VERSION JAJGST000000000.1 DBLINK BioProject: PRJNA774295 BioSample: SAMN22550082 KEYWORDS WGS. SOURCE Trogon surrucura (Suruca trogon) ORGANISM Trogon surrucura Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Trogoniformes; Trogonidae; Trogon. REFERENCE 1 (bases 1 to 182) AUTHORS Gilbert,M.T.P., Banin,D.A., Mountcastle,J., Balacco,J.R., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K., Graves,G., Fedrigo,O. and Jarvis,E.D. TITLE Trogon surrucura (Surucua trogon) genome, bTroSur1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 182) AUTHORS Gilbert,M.T.P., Banin,D.A., Mountcastle,J., Balacco,J.R., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K., Graves,G., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Trogon surrucura whole genome shotgun (WGS) project has the project accession JAJGST000000000. This version of the project (01) has the accession number JAJGST010000000, and consists of sequences JAJGST010000001-JAJGST010000182. ##Genome-Assembly-Data-START## Assembly Date :: 25-MAY-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deep variant polishing v. 1.1.0; gEVAL manual curation v. 2021-05-25; VGP pipeline v. 1.7 Assembly Name :: bTroSur1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 78.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Bionano Genomics Saphyr DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..182 /organism="Trogon surrucura" /mol_type="genomic DNA" /isolate="bTroSur1" /specimen_voucher="USNM 620787" /bio_material="B05987" /db_xref="taxon:297711" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="adult" /country="Argentina: Posadas, Misiones" /lat_lon="26.955278 S 55.087778 W" /collection_date="1995-10-29" /collected_by="D. A. Banin" WGS JAJGST010000001-JAJGST010000182 WGS_SCAFLD CM036617-CM036658 WGS_SCAFLD CM036751 // LOCUS JAJGQW010000000 146 rc DNA linear VRT 05-NOV-2021 DEFINITION Hemiprocne comata isolate bHemCom1, whole genome shotgun sequencing project. ACCESSION JAJGQW000000000 VERSION JAJGQW000000000.1 DBLINK BioProject: PRJNA774831 BioSample: SAMN22588383 KEYWORDS WGS. SOURCE Hemiprocne comata ORGANISM Hemiprocne comata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Apodiformes; Apodidae; Hemiprocninae; Hemiprocne. REFERENCE 1 (bases 1 to 146) AUTHORS Gilbert,M.T.P., Gaige,J., Haase,B., Mountcastle,J., Formenti,G., Phelan,S., Sims,Y., Ross,C., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Hemiprocne comata (whiskered treeswift) genome, bHemCom1 JOURNAL Unpublished REFERENCE 2 (bases 1 to 146) AUTHORS Gilbert,M.T.P., Gaige,J., Haase,B., Mountcastle,J., Formenti,G., Phelan,S., Sims,Y., Ross,C., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Hemiprocne comata whole genome shotgun (WGS) project has the project accession JAJGQW000000000. This version of the project (01) has the accession number JAJGQW010000000, and consists of sequences JAJGQW010000001-JAJGQW010000146. ##Genome-Assembly-Data-START## Assembly Date :: 24-SEP-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deepvariant polishing v. 1.1.0; gEVAL manual curation v. 2021-09-24; VGP pipeline v. 1.7 Assembly Name :: bHemCom1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 80.12x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Bionano Genomics DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..146 /organism="Hemiprocne comata" /mol_type="genomic DNA" /isolate="bHemCom1" /specimen_voucher="USNM 607338" /bio_material="B03790" /db_xref="taxon:243314" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="adult" /country="Philippines: Cagayan, Luzon Island (Barrio Via Sitio Hot Springs Baggao Mun.)" /lat_lon="17.85 N 121.98 E" /collection_date="1989-05-10" /collected_by="C. A. Ross" WGS JAJGQW010000001-JAJGQW010000146 WGS_SCAFLD CM036586-CM036616 WGS_SCAFLD CM036713 // LOCUS JAJGSR010000000 88 rc DNA linear VRT 05-NOV-2021 DEFINITION Theristicus caerulescens isolate bTheCae1, whole genome shotgun sequencing project. ACCESSION JAJGSR000000000 VERSION JAJGSR000000000.1 DBLINK BioProject: PRJNA774297 BioSample: SAMN22550094 KEYWORDS WGS. SOURCE Theristicus caerulescens (plumbeous ibis) ORGANISM Theristicus caerulescens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Pelecaniformes; Threskiornithidae; Theristicus. REFERENCE 1 (bases 1 to 88) AUTHORS Gilbert,M.T.P., Milensky,C., Mountcastle,J., Balacco,J., Formenti,G., Pelan,S., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Theristicus caerulescens (plumbeous ibis) genome, bTheCae1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 88) AUTHORS Gilbert,M.T.P., Milensky,C., Mountcastle,J., Balacco,J., Formenti,G., Pelan,S., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Theristicus caerulescens whole genome shotgun (WGS) project has the project accession JAJGSR000000000. This version of the project (01) has the accession number JAJGSR010000000, and consists of sequences JAJGSR010000001-JAJGSR010000088. ##Genome-Assembly-Data-START## Assembly Date :: 25-MAY-2021 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON unzip v. 7.0.1.66975; purge_dups v. 1.2.5; scaff10X v. 4.1.0; Bionano solve v. 3.4.0; Salsa2 v. 2.2; Arrow polishing pbcpp v. 1.9.0.1; Longranger Align v. 2.2.2; Deep variant polishing v. 1.1.0; gEVAL manual curation v. 2021-05-25; VGP pipeline v. 1.7 Assembly Name :: bTheCae1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 123.5x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Bionano Genomics Saphyr DLS; Arima Genomics Hi-C v1 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..88 /organism="Theristicus caerulescens" /mol_type="genomic DNA" /isolate="bTheCae1" /specimen_voucher="USNM 636095" /bio_material="B20749" /db_xref="taxon:1118847" /sex="female" /tissue_type="heart, muscle, liver" /dev_stage="juvenile chick" /country="Uruguay: Rocha" /lat_lon="33.741944 S 53.746111 W" /collection_date="2005-10-26" /collected_by="C. M. Milensky" WGS JAJGSR010000001-JAJGSR010000088 WGS_SCAFLD CM036558-CM036583 WGS_SCAFLD CM036585 // LOCUS JAJGSB010000000 508 rc DNA linear ROD 03-NOV-2021 DEFINITION Jaculus jaculus isolate mJacJac1, whole genome shotgun sequencing project. ACCESSION JAJGSB000000000 VERSION JAJGSB000000000.1 DBLINK BioProject: PRJNA773798 BioSample: SAMN20391724 KEYWORDS WGS. SOURCE Jaculus jaculus (lesser Egyptian jerboa) ORGANISM Jaculus jaculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Dipodoidea; Dipodidae; Dipodinae; Jaculus. REFERENCE 1 (bases 1 to 508) AUTHORS Copper,K., Brown,T., Winkler,S., Tracey,A., Sims,Y., Howe,K., Fedrigo,O., Jarvis,E.D. and Myers,G. TITLE Jaculus jaculus (Lesser Egyptian jerboa) genome, mJacJac1, paternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 508) AUTHORS Copper,K., Brown,T., Winkler,S., Tracey,A., Sims,Y., Howe,K., Fedrigo,O., Jarvis,E.D. and Myers,G. TITLE Direct Submission JOURNAL Submitted (01-NOV-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Jaculus jaculus whole genome shotgun (WGS) project has the project accession JAJGSB000000000. This version of the project (01) has the accession number JAJGSB010000000, and consists of sequences JAJGSB010000001-JAJGSB010000508. ##Genome-Assembly-Data-START## Assembly Date :: 2021 Assembly Method :: Trio HiCanu v. 2.1; purge_dups v. 1.2.3; Scaff10x v. 4.2; Bionano Solve v. 3.5.1; bwa v. 0.7.17; gcpp v. 1.9.0; Longranger Align v. 2.2.2; Freebayes v. 1.3.2; gEVAL manual curation v. 2021-05--07 Assembly Name :: mJacJac1.pat.decon Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 40.0x Sequencing Technology :: PacBio Sequel II CLR 101X; 10X Gemonics linked reads 78X; Bionano Genomics DLS 182X; Arima Genomics Hi-C v1 60X ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..508 /organism="Jaculus jaculus" /mol_type="genomic DNA" /isolate="mJacJac1" /db_xref="taxon:51337" /sex="male" /tissue_type="liver, spleen" /dev_stage="adult" /country="USA: San Diego" /lat_lon="32.72 N 117.17 W" /collection_date="2021-06-15" /collected_by="Kimberly Cooper" WGS JAJGSB010000001-JAJGSB010000508 // LOCUS JAJGSA010000000 159 rc DNA linear ROD 04-NOV-2021 DEFINITION Jaculus jaculus isolate mJacJac1, whole genome shotgun sequencing project. ACCESSION JAJGSA000000000 VERSION JAJGSA000000000.1 DBLINK BioProject: PRJNA773797 BioSample: SAMN20391724 KEYWORDS WGS. SOURCE Jaculus jaculus (lesser Egyptian jerboa) ORGANISM Jaculus jaculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Dipodoidea; Dipodidae; Dipodinae; Jaculus. REFERENCE 1 (bases 1 to 159) AUTHORS Cooper,K., Brown,T., Winkler,S., Tracey,A., Sims,Y., Howe,K., Fedrigo,O., Jarvis,E.D. and Myers,G. TITLE Jaculus jaculus (Lesser Egyptian jerboa) genome, mJacJac1, maternal + Y haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 159) AUTHORS Cooper,K., Brown,T., Winkler,S., Tracey,A., Sims,Y., Howe,K., Fedrigo,O., Jarvis,E.D. and Myers,G. TITLE Direct Submission JOURNAL Submitted (01-NOV-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Jaculus jaculus whole genome shotgun (WGS) project has the project accession JAJGSA000000000. This version of the project (01) has the accession number JAJGSA010000000, and consists of sequences JAJGSA010000001-JAJGSA010000159. ##Genome-Assembly-Data-START## Assembly Date :: 2021 Assembly Method :: Trio HiCanu v. 2.1; purge_dups v. 1.2.3; Scaff10x v. 4.2; Bionano Solve v. 3.5.1; bwa v. 0.7.17; gcpp v. 1.9.0; Longranger Align v. 2.2.2; Freebayes v. 1.3.2; gEVAL manual curation v. 2021-05--07 Assembly Name :: mJacJac1.mat.Y.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 61.0x Sequencing Technology :: PacBio Sequel II CLR 101X; 10X Gemonics linked reads 78X; Bionano Genomics DLS 182X; Arima Genomics Hi-C v1 60X ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..159 /organism="Jaculus jaculus" /mol_type="genomic DNA" /isolate="mJacJac1" /db_xref="taxon:51337" /sex="male" /tissue_type="liver, spleen" /dev_stage="adult" /country="USA: San Diego" /lat_lon="32.72 N 117.17 W" /collection_date="2021-06-15" /collected_by="Kimberly Cooper" WGS JAJGSA010000001-JAJGSA010000159 WGS_SCAFLD CM036389-CM036413 // LOCUS JAJGRB010000000 7527 rc DNA linear MAM 03-NOV-2021 DEFINITION Rhinolophus sinicus isolate mRhiSin1, whole genome shotgun sequencing project. ACCESSION JAJGRB000000000 VERSION JAJGRB000000000.1 DBLINK BioProject: PRJNA776468 BioSample: SAMN22787411 KEYWORDS WGS. SOURCE Rhinolophus sinicus (Chinese rufous horseshoe bat) ORGANISM Rhinolophus sinicus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus. REFERENCE 1 (bases 1 to 7527) AUTHORS Lu,J., Gao,D., Hu,Y., Huang,J., Collins,J., Sims,Y., Zhang,L., He,X., Liu,J., Fedrigo,O. and Jarvis,E.D. TITLE Rhinolophus sinicus (Chinese rufous horseshoe bat) genome, mRhiSin1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 7527) AUTHORS Lu,J., Gao,D., Hu,Y., Huang,J., Collins,J., Sims,Y., Zhang,L., He,X., Liu,J., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (30-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Rhinolophus sinicus whole genome shotgun (WGS) project has the project accession JAJGRB000000000. This version of the project (01) has the accession number JAJGRB010000000, and consists of sequences JAJGRB010000001-JAJGRB010007527. ##Genome-Assembly-Data-START## Assembly Date :: 20-SEP-2021 Assembly Method :: HiFiasm v. 0.12-r304; purge_dups v. 1.2.5; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.2; gEVAL manual curation v. 2021--09-20; VGP pipeline v. 2.0 Assembly Name :: mRhiSin1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 30.71x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7527 /organism="Rhinolophus sinicus" /mol_type="genomic DNA" /isolate="mRhiSin1" /db_xref="taxon:89399" /sex="female" /tissue_type="muscle" /dev_stage="adult" /country="China: Conghua, Guangzhou" /lat_lon="23.737583 N 113.842219 E" /collection_date="2020-02-13" /collected_by="Libiao Zhang" WGS JAJGRB010000001-JAJGRB010007527 // LOCUS JAJGSZ010000000 2762 rc DNA linear VRT 03-NOV-2021 DEFINITION Corvus hawaiiensis isolate bCorHaw1, whole genome shotgun sequencing project. ACCESSION JAJGSZ000000000 VERSION JAJGSZ000000000.1 DBLINK BioProject: PRJNA774316 BioSample: SAMN22550278 KEYWORDS WGS. SOURCE Corvus hawaiiensis (hawaiian crow) ORGANISM Corvus hawaiiensis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Corvoidea; Corvidae; Corvus. REFERENCE 1 (bases 1 to 2762) AUTHORS Grosser,S., Sutton,J., Masuda,B., Datlof,E., Ryder,O., Grueber,C., Formenti,G., Tracey,A., Pointon,D.-L., Wood,J., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Robertson,B. TITLE Corvus hawaiiensis (Hawaiian crow) genome, bCorHaw1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 2762) AUTHORS Grosser,S., Sutton,J., Masuda,B., Datlof,E., Ryder,O., Grueber,C., Formenti,G., Tracey,A., Pointon,D.-L., Wood,J., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Robertson,B. TITLE Direct Submission JOURNAL Submitted (01-NOV-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Corvus hawaiiensis whole genome shotgun (WGS) project has the project accession JAJGSZ000000000. This version of the project (01) has the accession number JAJGSZ010000000, and consists of sequences JAJGSZ010000001-JAJGSZ010002762. ##Genome-Assembly-Data-START## Assembly Date :: 20-SEP-2021 Assembly Method :: HiFiasm v. 0.15.4+galaxy; purge_dups v. 1.2.5+galaxy3; Bionano Solve v. 3.6.1+galaxy2; Salsa v. 2.3+galaxy0; gEVAL manual curation v. 2021-09-20; VGP pipeline v. 2.0 Assembly Name :: bCorHaw1.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 29.61x Sequencing Technology :: PacBio Sequel II HiFi; Illumina NovaSeq; Bionano Genomics DLS; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2762 /organism="Corvus hawaiiensis" /mol_type="genomic DNA" /isolate="bCorHaw1" /db_xref="taxon:134902" /sex="female" /tissue_type="blood" /dev_stage="adult" /country="USA: University of Hawaii at Manoa" /lat_lon="21.297467 N 157.818261 W" /collection_date="2020-08-08" /collected_by="Bryce Masuda" WGS JAJGSZ010000001-JAJGSZ010002762 // LOCUS JAJGQZ010000000 1697 rc DNA linear VRT 03-NOV-2021 DEFINITION Apus apus isolate bApuApu2, whole genome shotgun sequencing project. ACCESSION JAJGQZ000000000 VERSION JAJGQZ000000000.1 DBLINK BioProject: PRJNA776337 BioSample: SAMN22785356 KEYWORDS WGS. SOURCE Apus apus (common swift) ORGANISM Apus apus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Apodiformes; Apodidae; Apodinae; Apus. REFERENCE 1 (bases 1 to 1697) AUTHORS Hiller,M., Baldwin,M.W., Winkler,S., Ballerstaedt,N., Osipova,E., Sadanandan,K., Ko,M.-C., Sackton,T., Brown,T.F., Pippel,M., Tracey,A., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Apus apus (common swift) genome, bApuApu2, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1697) AUTHORS Hiller,M., Baldwin,M.W., Winkler,S., Ballerstaedt,N., Osipova,E., Sadanandan,K., Ko,M.-C., Sackton,T., Brown,T.F., Pippel,M., Tracey,A., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Apus apus whole genome shotgun (WGS) project has the project accession JAJGQZ000000000. This version of the project (01) has the accession number JAJGQZ010000000, and consists of sequences JAJGQZ010000001-JAJGQZ010001697. ##Genome-Assembly-Data-START## Assembly Date :: 17-JUN-2021 Assembly Method :: FALCON-kit v. 1.8.1; FALCON-Unzip v. 1.3.7; purge-dups v. 0.0.3; Longranger v. 2.2.2; scaff10X v. 4.2; Bionano solve v. 3.5.1; Salsa2 v. 2.2.0; dentist v. 1.0.0; Freebays v. 1.3.2; gEVAL manual curation v. 2021-06-17 Assembly Name :: bApuApu2.alt.cur Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 103.36x Sequencing Technology :: PacBio Sequel I CLR; Bionano Genomics DLS; Arima Genomics Hi-C; 10X Genomics linked reads ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1697 /organism="Apus apus" /mol_type="genomic DNA" /isolate="bApuApu2" /db_xref="taxon:8895" /sex="female" /tissue_type="Blood, muscle" /dev_stage="adult" /country="Germany: Tutzing" /lat_lon="47.969789 N 11.297823 E" /collection_date="2017-06-07" /collected_by="Maude W. Baldwin" WGS JAJGQZ010000001-JAJGQZ010001697 // LOCUS JAJGSY010000000 187 rc DNA linear VRT 04-NOV-2021 DEFINITION Corvus hawaiiensis isolate bCorHaw1, whole genome shotgun sequencing project. ACCESSION JAJGSY000000000 VERSION JAJGSY000000000.1 DBLINK BioProject: PRJNA774314 BioSample: SAMN22550278 KEYWORDS WGS. SOURCE Corvus hawaiiensis (hawaiian crow) ORGANISM Corvus hawaiiensis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Corvoidea; Corvidae; Corvus. REFERENCE 1 (bases 1 to 187) AUTHORS Grosser,S., Sutton,J., Masuda,B., Datlof,E., Ryder,O., Grueber,C., Formenti,G., Tracey,A., Pointon,D.-L., Wood,J., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Robertson,B. TITLE Corvus hawaiiensis (Hawaiian crow) genome, bCorHaw1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 187) AUTHORS Grosser,S., Sutton,J., Masuda,B., Datlof,E., Ryder,O., Grueber,C., Formenti,G., Tracey,A., Pointon,D.-L., Wood,J., Balacco,J., Mountcastle,J., Fedrigo,O., Jarvis,E.D. and Robertson,B. TITLE Direct Submission JOURNAL Submitted (30-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Corvus hawaiiensis whole genome shotgun (WGS) project has the project accession JAJGSY000000000. This version of the project (01) has the accession number JAJGSY010000000, and consists of sequences JAJGSY010000001-JAJGSY010000187. ##Genome-Assembly-Data-START## Assembly Date :: 20-SEP-2021 Assembly Method :: HiFiasm v. 0.15.4+galaxy; purge_dups v. 1.2.5+galaxy3; Bionano Solve v. 3.6.1+galaxy2; Salsa v. 2.3+galaxy0; gEVAL manual curation v. 2021-09-20; VGP pipeline v. 2.0 Assembly Name :: bCorHaw1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 29.61x Sequencing Technology :: PacBio Sequel II HiFi; Illumina NovaSeq; Bionano Genomics Saphyr DLS; Arima Genomics Hi-C v2 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..187 /organism="Corvus hawaiiensis" /mol_type="genomic DNA" /isolate="bCorHaw1" /db_xref="taxon:134902" /sex="female" /tissue_type="blood" /dev_stage="adult" /country="USA: University of Hawaii at Manoa" /lat_lon="21.297467 N 157.818261 W" /collection_date="2020-08-08" /collected_by="Bryce Masuda" WGS JAJGSY010000001-JAJGSY010000187 WGS_SCAFLD CM036346-CM036388 // LOCUS JAJGRA010000000 69 rc DNA linear MAM 04-NOV-2021 DEFINITION Rhinolophus sinicus isolate mRhiSin1, whole genome shotgun sequencing project. ACCESSION JAJGRA000000000 VERSION JAJGRA000000000.1 DBLINK BioProject: PRJNA776471 BioSample: SAMN22787411 KEYWORDS WGS. SOURCE Rhinolophus sinicus (Chinese rufous horseshoe bat) ORGANISM Rhinolophus sinicus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus. REFERENCE 1 (bases 1 to 69) AUTHORS Lu,J., Gao,D., Hu,Y., Huang,J., Collins,J., Sims,Y., Zhang,L., He,X., Liu,J., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Rhinolophus sinicus (Chinese rufous horseshoe bat) genome, mRhiSin1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 69) AUTHORS Lu,J., Gao,D., Hu,Y., Huang,J., Collins,J., Sims,Y., Zhang,L., He,X., Liu,J., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (30-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Rhinolophus sinicus whole genome shotgun (WGS) project has the project accession JAJGRA000000000. This version of the project (01) has the accession number JAJGRA010000000, and consists of sequences JAJGRA010000001-JAJGRA010000069. ##Genome-Assembly-Data-START## Assembly Date :: 20-SEP-2021 Assembly Method :: HiFiasm v. 0.12-r304; purge_dups v. 1.2.5; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.2; gEVAL manual curation v. 2021--09-20; VGP pipeline v. 2.0 Assembly Name :: mRhiSin1.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 30.71x Sequencing Technology :: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..69 /organism="Rhinolophus sinicus" /mol_type="genomic DNA" /isolate="mRhiSin1" /db_xref="taxon:89399" /sex="female" /tissue_type="muscle" /dev_stage="adult" /country="China: Conghua, Guangzhou" /lat_lon="23.737583 N 113.842219 E" /collection_date="2020-02-13" /collected_by="Libiao Zhang" WGS JAJGRA010000001-JAJGRA010000069 WGS_SCAFLD CM036414-CM036431 // LOCUS JAJGPZ010000000 312 rc DNA linear PRI 03-NOV-2021 DEFINITION Lemur catta isolate mLemCat1, whole genome shotgun sequencing project. ACCESSION JAJGPZ000000000 VERSION JAJGPZ000000000.1 DBLINK BioProject: PRJNA561950 BioSample: SAMN12621102 KEYWORDS WGS. SOURCE Lemur catta (Ring-tailed lemur) ORGANISM Lemur catta Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Strepsirrhini; Lemuriformes; Lemuridae; Lemur. REFERENCE 1 (bases 1 to 312) AUTHORS Marques,T., Balacco,J., Formenti,G., Palmada,M., Orkin,J., Kuderna,L., Mountcastle,J., Haase,B., Bertelsen,M., Gilbert,M.T.P., Sims,Y., Wood,J., Fedrigo,O. and Jarvis,E.D. TITLE Lemur catta (Ring-tailed lemur) genome, mLemCat1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 312) AUTHORS Marques,T., Balacco,J., Formenti,G., Palmada,M., Orkin,J., Kuderna,L., Mountcastle,J., Haase,B., Bertelsen,M., Gilbert,M.T.P., Sims,Y., Wood,J., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (23-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Lemur catta whole genome shotgun (WGS) project has the project accession JAJGPZ000000000. This version of the project (01) has the accession number JAJGPZ010000000, and consists of sequences JAJGPZ010000001-JAJGPZ010000312. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: hifiasm v. 0.12-r304; purge_dups v. 1.2.5; bionano_solve Solve v. 3.6.1; salsa2 v. v2.2; gEVAL manual curation v. 2021-07-16 Assembly Name :: mLemCat1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 20.81x Sequencing Technology :: Pacbio Sequel II CCS; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics v1 Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..312 /organism="Lemur catta" /mol_type="genomic DNA" /isolate="mLemCat1" /db_xref="taxon:9447" /sex="male" /tissue_type="spleen" /dev_stage="juvenile" /country="Denmark: Copenhagen Zoo" /lat_lon="55.67278 N 12.52139 E" /collection_date="2015-12-16" /collected_by="Mads Bertelsen" WGS JAJGPZ010000001-JAJGPZ010000312 // LOCUS JAJGPY010000000 185 rc DNA linear PRI 04-NOV-2021 DEFINITION Lemur catta isolate mLemCat1, whole genome shotgun sequencing project. ACCESSION JAJGPY000000000 VERSION JAJGPY000000000.1 DBLINK BioProject: PRJNA561949 BioSample: SAMN12621102 KEYWORDS WGS. SOURCE Lemur catta (Ring-tailed lemur) ORGANISM Lemur catta Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Strepsirrhini; Lemuriformes; Lemuridae; Lemur. REFERENCE 1 (bases 1 to 185) AUTHORS Marques,T., Balacco,J., Formenti,G., Palmada,M., Orkin,J., Kuderna,L., Mountcastle,J., Haase,B., Bertelsen,M., Gilbert,M.T.P., Tracey,A., Sims,Y., Wood,J., Fedrigo,O. and Jarvis,E.D. TITLE Lemur catta (Ring-tailed lemur) genome, mLemCat1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 185) AUTHORS Marques,T., Balacco,J., Formenti,G., Palmada,M., Orkin,J., Kuderna,L., Mountcastle,J., Haase,B., Bertelsen,M., Gilbert,M.T.P., Tracey,A., Sims,Y., Wood,J., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (28-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Lemur catta whole genome shotgun (WGS) project has the project accession JAJGPY000000000. This version of the project (01) has the accession number JAJGPY010000000, and consists of sequences JAJGPY010000001-JAJGPY010000185. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: hifiasm v. 0.12-r304; purge_dups v. 1.2.5; bionano_solve v. Solve3.6.1_11162020; salsa2 v. v2.2; gEVAL manual curation v. 2021-07-16 Assembly Name :: mLemCat1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 20.81x Sequencing Technology :: Pacbio Sequel II CCS; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics v1 Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..185 /organism="Lemur catta" /mol_type="genomic DNA" /isolate="mLemCat1" /db_xref="taxon:9447" /sex="male" /tissue_type="spleen" /dev_stage="juvenile" /country="Denmark: Copenhagen Zoo" /lat_lon="55.67278 N 12.52139 E" /collection_date="2015-12-16" /collected_by="Mads Bertelsen" WGS JAJGPY010000001-JAJGPY010000185 WGS_SCAFLD CM036472-CM036500 WGS_SCAFLD CM036502 // LOCUS JAJGQY010000000 109 rc DNA linear VRT 04-NOV-2021 DEFINITION Apus apus isolate bApuApu2, whole genome shotgun sequencing project. ACCESSION JAJGQY000000000 VERSION JAJGQY000000000.1 DBLINK BioProject: PRJNA776336 BioSample: SAMN22785356 KEYWORDS WGS. SOURCE Apus apus (common swift) ORGANISM Apus apus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Apodiformes; Apodidae; Apodinae; Apus. REFERENCE 1 (bases 1 to 109) AUTHORS Hiller,M., Baldwin,M.W., Winkler,S., Ballerstaedt,N., Osipova,E., Sadanandan,K., Ko,M.-C., Sackton,T., Brown,T.F., Pippel,M., Tracey,A., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Apus apus (common swift) genome, bApuApu2, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 109) AUTHORS Hiller,M., Baldwin,M.W., Winkler,S., Ballerstaedt,N., Osipova,E., Sadanandan,K., Ko,M.-C., Sackton,T., Brown,T.F., Pippel,M., Tracey,A., Sims,Y., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Apus apus whole genome shotgun (WGS) project has the project accession JAJGQY000000000. This version of the project (01) has the accession number JAJGQY010000000, and consists of sequences JAJGQY010000001-JAJGQY010000109. ##Genome-Assembly-Data-START## Assembly Date :: 17-JUN-2021 Assembly Method :: FALCON-kit v. 1.8.1; FALCON-Unzip v. 1.3.7; purge-dups v. 0.0.3; Longranger v. 2.2.2; scaff10X v. 4.2; Bionano solve v. 3.5.1; Salsa2 v. 2.2.0; dentist v. 1.0.0; Freebays v. 1.3.2; gEVAL manual curation v. 2021-06-17 Assembly Name :: bApuApu2.pri.cur Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 103.36x Sequencing Technology :: PacBio Sequel I CLR; Bionano Genomics DLS; Arima Genomics Hi-C; 10X Genomics linked reads ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..109 /organism="Apus apus" /mol_type="genomic DNA" /isolate="bApuApu2" /db_xref="taxon:8895" /sex="female" /tissue_type="Blood, muscle" /dev_stage="adult" /country="Germany: Tutzing" /lat_lon="47.969789 N 11.297823 E" /collection_date="2017-06-07" /collected_by="Maude W. Baldwin" WGS JAJGQY010000001-JAJGQY010000109 WGS_SCAFLD CM036503-CM036533 // LOCUS WPOB02000000 3096 rc DNA linear MAM 02-NOV-2021 DEFINITION Zalophus californianus isolate mZalCal1, whole genome shotgun sequencing project. ACCESSION WPOB00000000 VERSION WPOB00000000.2 DBLINK BioProject: PRJNA559674 BioSample: SAMN12368149 KEYWORDS WGS. SOURCE Zalophus californianus (California sea lion) ORGANISM Zalophus californianus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Otariidae; Zalophus. REFERENCE 1 (bases 1 to 3096) AUTHORS Peart,C.R., Williams,C., Pophaly,S.D., Neely,B.A., Gulland,F.M.D., Adams,D.J., Ng,B.L., Cheng,W., Goebel,M.E., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Collins,J., Wood,J., Sims,Y., Torrance,J., Tracey,A., Howe,K., Rhie,A., Hoffman,J.I., Johnson,J., Jarvis,E.D., Breen,M. and Wolf,J.B.W. TITLE Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution JOURNAL Mol Ecol Resour 21 (7), 2455-2470 (2021) PUBMED 34097816 REFERENCE 2 (bases 1 to 3096) AUTHORS Wolf,J., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Gulland,F., Mcclain,A., Peart,C., Tracey,A., Sims,Y., Howe,K., Rhie,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-NOV-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 3096) AUTHORS Wolf,J., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Gulland,F., Mcclain,A., Peart,C., Tracey,A., Sims,Y., Howe,K., Rhie,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (31-MAY-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Jun 12, 2020 this sequence version replaced WPOB00000000.1. The Zalophus californianus whole genome shotgun (WGS) project has the project accession WPOB00000000. This version of the project (02) has the accession number WPOB02000000, and consists of sequences WPOB02000001-WPOB02003096. This assembly represents the alternate haplotype of the diploid genome Zalophus californianus. The principal haplotype sequences are in WGS project WPOA00000000. ##Genome-Assembly-Data-START## Assembly Date :: 13-MAR-2020 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 7.0.1.66975; purge_dups v. v1; scaff10x v. 4.1.0; Bionano Solve DLS v. 3.2.1; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. SMRTLink7.0.1; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2020-03-13; VGP assembly pipeline individual v. 1.6 Assembly Name :: mZalCal1.alt.v2 Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 80.51x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..3096 /organism="Zalophus californianus" /mol_type="genomic DNA" /isolate="mZalCal1" /db_xref="taxon:9704" /sex="male" /tissue_type="blood" /country="USA: California" /lat_lon="37.858768 N 122.484010 W" /collection_date="07-Jul-2018" /collected_by="Frances Gulland and Jochen Wolf" WGS WPOB02000001-WPOB02003096 // LOCUS WPOA02000000 47 rc DNA linear MAM 02-NOV-2021 DEFINITION Zalophus californianus isolate mZalCal1, whole genome shotgun sequencing project. ACCESSION WPOA00000000 VERSION WPOA00000000.2 DBLINK BioProject: PRJNA559673 BioSample: SAMN12368149 KEYWORDS WGS. SOURCE Zalophus californianus (California sea lion) ORGANISM Zalophus californianus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Otariidae; Zalophus. REFERENCE 1 (bases 1 to 47) AUTHORS Peart,C.R., Williams,C., Pophaly,S.D., Neely,B.A., Gulland,F.M.D., Adams,D.J., Ng,B.L., Cheng,W., Goebel,M.E., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Collins,J., Wood,J., Sims,Y., Torrance,J., Tracey,A., Howe,K., Rhie,A., Hoffman,J.I., Johnson,J., Jarvis,E.D., Breen,M. and Wolf,J.B.W. TITLE Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution JOURNAL Mol Ecol Resour 21 (7), 2455-2470 (2021) PUBMED 34097816 REFERENCE 2 (bases 1 to 47) AUTHORS Wolf,J., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Gulland,F., Mcclain,A., Peart,C., Tracey,A., Sims,Y., Howe,K., Rhie,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (29-NOV-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 47) AUTHORS Wolf,J., Fedrigo,O., Haase,B., Mountcastle,J., Fungtammasan,A., Formenti,G., Gulland,F., Mcclain,A., Peart,C., Tracey,A., Sims,Y., Howe,K., Rhie,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (05-JUN-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Jun 12, 2020 this sequence version replaced WPOA00000000.1. The Zalophus californianus whole genome shotgun (WGS) project has the project accession WPOA00000000. This version of the project (02) has the accession number WPOA02000000, and consists of sequences WPOA02000001-WPOA02000047. This assembly represents the principal haplotype of the diploid genome Zalophus californianus and includes the chromosomes. The alternate haplotype sequences are in WGS project WPOB00000000. ##Genome-Assembly-Data-START## Assembly Date :: 13-MAR-2020 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 7.0.1.66975; purge_dups v. v1; scaff10x v. 4.1.0; Bionano Solve DLS v. 3.2.1; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. SMRTLink7.0.1; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2020-03-13; VGP assembly pipeline individual v. 1.6 Assembly Name :: mZalCal1.pri.v2 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 80.51x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..47 /organism="Zalophus californianus" /mol_type="genomic DNA" /isolate="mZalCal1" /db_xref="taxon:9704" /sex="male" /tissue_type="blood" /country="USA: California" /lat_lon="37.858768 N 122.484010 W" /collection_date="07-Jul-2018" /collected_by="Frances Gulland and Jochen Wolf" WGS WPOA02000001-WPOA02000047 WGS_SCAFLD CM019802-CM019821 // LOCUS CAKJTE010000000 158 rc DNA linear INV 14-OCT-2021 DEFINITION Limnephilus lunatus, whole genome shotgun sequencing project. ACCESSION CAKJTE000000000 VERSION CAKJTE000000000.1 DBLINK BioProject: PRJEB48033 BioSample: SAMEA7521206 Sequence Read Archive: ERR6688475, ERR6688476, ERR6688477, ERR6688478, ERR6688479, ERR6688481, ERR6688482, ERR6688483, ERR6688484, ERR6907853, ERR6939235 KEYWORDS WGS. SOURCE Limnephilus lunatus ORGANISM Limnephilus lunatus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Trichoptera; Integripalpia; Plenitentoria; Limnephiloidea; Limnephilidae; Limnephilinae; Limnephilini; Limnephilus. REFERENCE 1 (bases 1 to 158) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (12-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Limnephilus lunatus whole genome shotgun (WGS) project has the project accession CAKJTE000000000. This version of the project (01) has the accession number CAKJTE010000000, and consists of sequences CAKJTE010000001-CAKJTE010000158. The assembly iiLimLuna2.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Inversions between haplotypes observed on chromosome 3 104.64-110.84mb, chromosome 11 2.56-20.55mb. FEATURES Location/Qualifiers source 1..158 /organism="Limnephilus lunatus" /mol_type="genomic DNA" /db_xref="taxon:1218281" WGS CAKJTE010000001-CAKJTE010000158 // LOCUS CAJHXC020000000 927 rc DNA linear INV 13-OCT-2021 DEFINITION Xestia xanthographa, whole genome shotgun sequencing project. ACCESSION CAJHXC000000000 VERSION CAJHXC000000000.2 DBLINK BioProject: PRJEB41958 BioSample: SAMEA7520195 KEYWORDS WGS. SOURCE Xestia xanthographa ORGANISM Xestia xanthographa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Xestia. REFERENCE 1 (bases 1 to 927) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 927) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (24-AUG-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Oct 15, 2021 this sequence version replaced CAJHXC000000000.1. The Xestia xanthographa whole genome shotgun (WGS) project has the project accession CAJHXC000000000. This version of the project (02) has the accession number CAJHXC020000000, and consists of sequences CAJHXC020000001-CAJHXC020000927. The assembly ilXesXant1.2 is based on 27x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..927 /organism="Xestia xanthographa" /mol_type="genomic DNA" /db_xref="taxon:988049" WGS CAJHXC020000001-CAJHXC020000927 // LOCUS CAKJSY010000000 596 rc DNA linear INV 13-OCT-2021 DEFINITION Dryobotodes eremita, whole genome shotgun sequencing project. ACCESSION CAKJSY000000000 VERSION CAKJSY000000000.1 DBLINK BioProject: PRJEB48056 BioSample: SAMEA8603190 Sequence Read Archive: ERR6688524, ERR6688525, ERR6688526, ERR6688527, ERR6688528, ERR6808003 KEYWORDS WGS. SOURCE Dryobotodes eremita ORGANISM Dryobotodes eremita Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Dryobotodes. REFERENCE 1 (bases 1 to 596) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dryobotodes eremita whole genome shotgun (WGS) project has the project accession CAKJSY000000000. This version of the project (01) has the accession number CAKJSY010000000, and consists of sequences CAKJSY010000001-CAKJSY010000596. The assembly ilDryErem1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..596 /organism="Dryobotodes eremita" /mol_type="genomic DNA" /db_xref="taxon:988106" WGS CAKJSY010000001-CAKJSY010000596 // LOCUS CAKJSX010000000 341 rc DNA linear INV 13-OCT-2021 DEFINITION Orgyia antiqua, whole genome shotgun sequencing project. ACCESSION CAKJSX000000000 VERSION CAKJSX000000000.1 DBLINK BioProject: PRJEB47959 BioSample: SAMEA7524390 KEYWORDS WGS. SOURCE Orgyia antiqua (rusty tussock moth) ORGANISM Orgyia antiqua Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Lymantriinae; Orgyia. REFERENCE 1 (bases 1 to 341) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (06-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Orgyia antiqua whole genome shotgun (WGS) project has the project accession CAKJSX000000000. This version of the project (01) has the accession number CAKJSX010000000, and consists of sequences CAKJSX010000001-CAKJSX010000341. The assembly ilOrgAnti1.1 is based on 14x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..341 /organism="Orgyia antiqua" /mol_type="genomic DNA" /db_xref="taxon:335469" WGS CAKJSX010000001-CAKJSX010000341 // LOCUS CAKJTB010000000 2677 rc DNA linear INV 13-OCT-2021 DEFINITION Ichneumon xanthorius, whole genome shotgun sequencing project. ACCESSION CAKJTB000000000 VERSION CAKJTB000000000.1 DBLINK BioProject: PRJEB48053 BioSample: SAMEA7746465 Sequence Read Archive: ERR6688585, ERR6688586, ERR6688587, ERR6688588, ERR6688589, ERR6808013 KEYWORDS WGS. SOURCE Ichneumon xanthorius ORGANISM Ichneumon xanthorius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Parasitoida; Ichneumonoidea; Ichneumonidae; Ichneumoninae; Ichneumon. REFERENCE 1 (bases 1 to 2677) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ichneumon xanthorius whole genome shotgun (WGS) project has the project accession CAKJTB000000000. This version of the project (01) has the accession number CAKJTB010000000, and consists of sequences CAKJTB010000001-CAKJTB010002677. The assembly iyIchXant1.1 is based on 55x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The orientation of chromosome 10 1.08-1.74mb cannot be determined from available data. FEATURES Location/Qualifiers source 1..2677 /organism="Ichneumon xanthorius" /mol_type="genomic DNA" /db_xref="taxon:2795680" WGS CAKJTB010000001-CAKJTB010002677 // LOCUS CAKJTD010000000 138 rc DNA linear INV 13-OCT-2021 DEFINITION Ichneumon xanthorius, whole genome shotgun sequencing project. ACCESSION CAKJTD000000000 VERSION CAKJTD000000000.1 DBLINK BioProject: PRJEB48052 BioSample: SAMEA7746465 Sequence Read Archive: ERR6688585, ERR6688586, ERR6688587, ERR6688588, ERR6688589, ERR6808013 KEYWORDS WGS. SOURCE Ichneumon xanthorius ORGANISM Ichneumon xanthorius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Parasitoida; Ichneumonoidea; Ichneumonidae; Ichneumoninae; Ichneumon. REFERENCE 1 (bases 1 to 138) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ichneumon xanthorius whole genome shotgun (WGS) project has the project accession CAKJTD000000000. This version of the project (01) has the accession number CAKJTD010000000, and consists of sequences CAKJTD010000001-CAKJTD010000138. The assembly iyIchXant1.1 is based on 55x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The orientation of chromosome 10 1.08-1.74mb cannot be determined from available data. FEATURES Location/Qualifiers source 1..138 /organism="Ichneumon xanthorius" /mol_type="genomic DNA" /db_xref="taxon:2795680" WGS CAKJTD010000001-CAKJTD010000138 // LOCUS CAJYYF010000000 27 rc DNA linear INV 13-OCT-2021 DEFINITION Seladonia tumulorum, whole genome shotgun sequencing project. ACCESSION CAJYYF000000000 VERSION CAJYYF000000000.1 DBLINK BioProject: PRJEB47128 BioSample: SAMEA7746445 KEYWORDS WGS. SOURCE Seladonia tumulorum ORGANISM Seladonia tumulorum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Seladonia. REFERENCE 1 (bases 1 to 27) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (23-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Seladonia tumulorum whole genome shotgun (WGS) project has the project accession CAJYYF000000000. This version of the project (01) has the accession number CAJYYF010000000, and consists of sequences CAJYYF010000001-CAJYYF010000027. The assembly iySelTumu1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. HiC associations between chromosome arms were very faint leaving some room for potentially missing joins. No karyotype was found, leaving a small amount of uncertainty over the final number of chromosome we identified. FEATURES Location/Qualifiers source 1..27 /organism="Seladonia tumulorum" /mol_type="genomic DNA" /db_xref="taxon:115100" WGS CAJYYF010000001-CAJYYF010000027 // LOCUS CAJYYH010000000 109 rc DNA linear INV 13-OCT-2021 DEFINITION Seladonia tumulorum, whole genome shotgun sequencing project. ACCESSION CAJYYH000000000 VERSION CAJYYH000000000.1 DBLINK BioProject: PRJEB47129 BioSample: SAMEA7746445 KEYWORDS WGS. SOURCE Seladonia tumulorum ORGANISM Seladonia tumulorum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Seladonia. REFERENCE 1 (bases 1 to 109) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (23-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Seladonia tumulorum whole genome shotgun (WGS) project has the project accession CAJYYH000000000. This version of the project (01) has the accession number CAJYYH010000000, and consists of sequences CAJYYH010000001-CAJYYH010000109. The assembly iySelTumu1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. HiC associations between chromosome arms were very faint leaving some room for potentially missing joins. No karyotype was found, leaving a small amount of uncertainty over the final number of chromosome we identified. FEATURES Location/Qualifiers source 1..109 /organism="Seladonia tumulorum" /mol_type="genomic DNA" /db_xref="taxon:115100" WGS CAJYYH010000001-CAJYYH010000109 // LOCUS CAKJTC010000000 285 rc DNA linear INV 13-OCT-2021 DEFINITION Mimumesa dahlbomi, whole genome shotgun sequencing project. ACCESSION CAKJTC000000000 VERSION CAKJTC000000000.1 DBLINK BioProject: PRJEB48054 BioSample: SAMEA8603165 Sequence Read Archive: ERR6688575, ERR6688576, ERR6688577, ERR6688578, ERR6688579, ERR6808011 KEYWORDS WGS. SOURCE Mimumesa dahlbomi ORGANISM Mimumesa dahlbomi Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Pemphredoninae; Psenini; Mimumesa. REFERENCE 1 (bases 1 to 285) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mimumesa dahlbomi whole genome shotgun (WGS) project has the project accession CAKJTC000000000. This version of the project (01) has the accession number CAKJTC010000000, and consists of sequences CAKJTC010000001-CAKJTC010000285. The assembly iyMimDahl1.1 is based on 52x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..285 /organism="Mimumesa dahlbomi" /mol_type="genomic DNA" /db_xref="taxon:2495085" WGS CAKJTC010000001-CAKJTC010000285 // LOCUS CAJYYI010000000 375 rc DNA linear INV 13-OCT-2021 DEFINITION Sphecodes monilicornis, whole genome shotgun sequencing project. ACCESSION CAJYYI000000000 VERSION CAJYYI000000000.1 DBLINK BioProject: PRJEB47131 BioSample: SAMEA7746755 KEYWORDS WGS. SOURCE Sphecodes monilicornis ORGANISM Sphecodes monilicornis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Sphecodini; Sphecodes. REFERENCE 1 (bases 1 to 375) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (23-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sphecodes monilicornis whole genome shotgun (WGS) project has the project accession CAJYYI000000000. This version of the project (01) has the accession number CAJYYI010000000, and consists of sequences CAJYYI010000001-CAJYYI010000375. The assembly iySphMoni1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..375 /organism="Sphecodes monilicornis" /mol_type="genomic DNA" /db_xref="taxon:1190790" WGS CAJYYI010000001-CAJYYI010000375 // LOCUS CAKJTF010000000 51 rc DNA linear INV 14-OCT-2021 DEFINITION Limnephilus lunatus, whole genome shotgun sequencing project. ACCESSION CAKJTF000000000 VERSION CAKJTF000000000.1 DBLINK BioProject: PRJEB48032 BioSample: SAMEA7521206 Sequence Read Archive: ERR6688475, ERR6688476, ERR6688477, ERR6688478, ERR6688479, ERR6688481, ERR6688482, ERR6688483, ERR6688484, ERR6907853, ERR6939235 KEYWORDS WGS. SOURCE Limnephilus lunatus ORGANISM Limnephilus lunatus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Trichoptera; Integripalpia; Plenitentoria; Limnephiloidea; Limnephilidae; Limnephilinae; Limnephilini; Limnephilus. REFERENCE 1 (bases 1 to 51) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (12-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Limnephilus lunatus whole genome shotgun (WGS) project has the project accession CAKJTF000000000. This version of the project (01) has the accession number CAKJTF010000000, and consists of sequences CAKJTF010000001-CAKJTF010000051. The assembly iiLimLuna2.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Inversions between haplotypes observed on chromosome 3 104.64-110.84mb, chromosome 11 2.56-20.55mb. FEATURES Location/Qualifiers source 1..51 /organism="Limnephilus lunatus" /mol_type="genomic DNA" /db_xref="taxon:1218281" WGS CAKJTF010000001-CAKJTF010000051 // LOCUS CAKJSZ010000000 35 rc DNA linear INV 13-OCT-2021 DEFINITION Dryobotodes eremita, whole genome shotgun sequencing project. ACCESSION CAKJSZ000000000 VERSION CAKJSZ000000000.1 DBLINK BioProject: PRJEB48057 BioSample: SAMEA8603190 Sequence Read Archive: ERR6688524, ERR6688525, ERR6688526, ERR6688527, ERR6688528, ERR6808003 KEYWORDS WGS. SOURCE Dryobotodes eremita ORGANISM Dryobotodes eremita Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Dryobotodes. REFERENCE 1 (bases 1 to 35) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dryobotodes eremita whole genome shotgun (WGS) project has the project accession CAKJSZ000000000. This version of the project (01) has the accession number CAKJSZ010000000, and consists of sequences CAKJSZ010000001-CAKJSZ010000035. The assembly ilDryErem1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..35 /organism="Dryobotodes eremita" /mol_type="genomic DNA" /db_xref="taxon:988106" WGS CAKJSZ010000001-CAKJSZ010000035 // LOCUS CAKJTA010000000 59 rc DNA linear INV 13-OCT-2021 DEFINITION Mimumesa dahlbomi, whole genome shotgun sequencing project. ACCESSION CAKJTA000000000 VERSION CAKJTA000000000.1 DBLINK BioProject: PRJEB48055 BioSample: SAMEA8603165 Sequence Read Archive: ERR6688575, ERR6688576, ERR6688577, ERR6688578, ERR6688579, ERR6808011 KEYWORDS WGS. SOURCE Mimumesa dahlbomi ORGANISM Mimumesa dahlbomi Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Pemphredoninae; Psenini; Mimumesa. REFERENCE 1 (bases 1 to 59) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (11-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mimumesa dahlbomi whole genome shotgun (WGS) project has the project accession CAKJTA000000000. This version of the project (01) has the accession number CAKJTA010000000, and consists of sequences CAKJTA010000001-CAKJTA010000059. The assembly iyMimDahl1.1 is based on 52x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..59 /organism="Mimumesa dahlbomi" /mol_type="genomic DNA" /db_xref="taxon:2495085" WGS CAKJTA010000001-CAKJTA010000059 // LOCUS CAJYYG010000000 180 rc DNA linear INV 13-OCT-2021 DEFINITION Sphecodes monilicornis, whole genome shotgun sequencing project. ACCESSION CAJYYG000000000 VERSION CAJYYG000000000.1 DBLINK BioProject: PRJEB47130 BioSample: SAMEA7746755 KEYWORDS WGS. SOURCE Sphecodes monilicornis ORGANISM Sphecodes monilicornis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Sphecodini; Sphecodes. REFERENCE 1 (bases 1 to 180) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (23-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sphecodes monilicornis whole genome shotgun (WGS) project has the project accession CAJYYG000000000. This version of the project (01) has the accession number CAJYYG010000000, and consists of sequences CAJYYG010000001-CAJYYG010000180. The assembly iySphMoni1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..180 /organism="Sphecodes monilicornis" /mol_type="genomic DNA" /db_xref="taxon:1190790" WGS CAJYYG010000001-CAJYYG010000180 // LOCUS CAJHXD020000000 27 rc DNA linear INV 13-OCT-2021 DEFINITION Xestia xanthographa, whole genome shotgun sequencing project. ACCESSION CAJHXD000000000 VERSION CAJHXD000000000.2 DBLINK BioProject: PRJEB41957 BioSample: SAMEA7520195 KEYWORDS WGS. SOURCE Xestia xanthographa ORGANISM Xestia xanthographa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Xestia. REFERENCE 1 (bases 1 to 27) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 27) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (24-AUG-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Oct 15, 2021 this sequence version replaced CAJHXD000000000.1. The Xestia xanthographa whole genome shotgun (WGS) project has the project accession CAJHXD000000000. This version of the project (02) has the accession number CAJHXD020000000, and consists of sequences CAJHXD020000001-CAJHXD020000027. The assembly ilXesXant1.2 is based on 27x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..27 /organism="Xestia xanthographa" /mol_type="genomic DNA" /db_xref="taxon:988049" WGS CAJHXD020000001-CAJHXD020000027 // LOCUS JAJAQG010000000 21417 rc DNA linear VRT 15-OCT-2021 DEFINITION Pholidichthys leucotaenia isolate fPhoLeu1, whole genome shotgun sequencing project. ACCESSION JAJAQG000000000 VERSION JAJAQG000000000.1 DBLINK BioProject: PRJNA749576 BioSample: SAMN12623617 KEYWORDS WGS. SOURCE Pholidichthys leucotaenia ORGANISM Pholidichthys leucotaenia Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Cichlomorphae; Cichliformes; Pholidichthyidae; Pholidichthys. REFERENCE 1 (bases 1 to 21417) AUTHORS Myers,G., Brown,T., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Byrappa,V., Fedrigo,O., Jarvis,E.D. and Durbin,R. TITLE Pholidichthys leucotaenia (Convict blenny) genome, fPhoLeu1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 21417) AUTHORS Myers,G., Brown,T., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Byrappa,V., Fedrigo,O., Jarvis,E.D. and Durbin,R. TITLE Direct Submission JOURNAL Submitted (02-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Pholidichthys leucotaenia whole genome shotgun (WGS) project has the project accession JAJAQG000000000. This version of the project (01) has the accession number JAJAQG010000000, and consists of sequences JAJAQG010000001-JAJAQG010021417. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: falcon-kit v. 1.3.0; FALCON-Unzip v. 1.2.0; purge_dups v. 1.2.3; scaff10X v. 4.2; bionano Solve Solve v. 3.5_12162019; Salsa2 HiC v. 2.2; Longranger Align v. 2.2.2; pbmm2 v. 1.4.0; gcpp v. 1.0.0-1807624; bcftools v. 1.12-21-ga865a16; merfin v. 09c026d; deepvariant v. 1.1.0; gEVAL manual curation v. 2021-07-16 Assembly Name :: fPhoLeu1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 98.18x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..21417 /organism="Pholidichthys leucotaenia" /mol_type="genomic DNA" /isolate="fPhoLeu1" /db_xref="taxon:390368" /tissue_type="whole body" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-23" /collected_by="Byrappa Venkatesh" WGS JAJAQG010000001-JAJAQG010021417 // LOCUS JAJAQF010000000 512 rc DNA linear VRT 15-OCT-2021 DEFINITION Pholidichthys leucotaenia isolate fPhoLeu1, whole genome shotgun sequencing project. ACCESSION JAJAQF000000000 VERSION JAJAQF000000000.1 DBLINK BioProject: PRJNA749575 BioSample: SAMN12623617 KEYWORDS WGS. SOURCE Pholidichthys leucotaenia ORGANISM Pholidichthys leucotaenia Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Cichlomorphae; Cichliformes; Pholidichthyidae; Pholidichthys. REFERENCE 1 (bases 1 to 512) AUTHORS Myers,G., Brown,T., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Jarvis,E.D. and Durbin,R. TITLE Pholidichthys leucotaenia (Convict blenny) genome, fPhoLeu1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 512) AUTHORS Myers,G., Brown,T., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Jarvis,E.D. and Durbin,R. TITLE Direct Submission JOURNAL Submitted (02-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Pholidichthys leucotaenia whole genome shotgun (WGS) project has the project accession JAJAQF000000000. This version of the project (01) has the accession number JAJAQF010000000, and consists of sequences JAJAQF010000001-JAJAQF010000512. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: falcon-kit v. 1.3.0; FALCON-Unzip v. 1.2.0; purge_dups v. 1.2.3; scaff10X v. 4.2; bionano Solve Solve v. 3.5_12162019; Salsa2 HiC v. 2.2; Longranger Align v. 2.2.2; pbmm2 v. 1.4.0; gcpp v. 1.0.0-1807624; bcftools v. 1.12-21-ga865a16; merfin v. 09c026d; deepvariant v. 1.1.0; gEVAL manual curation v. 2021-07-16 Assembly Name :: fPhoLeu1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 98.18x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..512 /organism="Pholidichthys leucotaenia" /mol_type="genomic DNA" /isolate="fPhoLeu1" /db_xref="taxon:390368" /tissue_type="whole body" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-23" /collected_by="Byrappa Venkatesh" WGS JAJAQF010000001-JAJAQF010000512 WGS_SCAFLD CM035836-CM035850 // LOCUS CAKJPO010000000 1529 rc DNA linear INV 11-OCT-2021 DEFINITION Patella pellucida, whole genome shotgun sequencing project. ACCESSION CAKJPO000000000 VERSION CAKJPO000000000.1 DBLINK BioProject: PRJEB47995 BioSample: SAMEA7522851 Sequence Read Archive: ERR6054924, ERR6054925, ERR6054926, ERR6054927, ERR6054928, ERR6054929, ERR6412040 KEYWORDS WGS. SOURCE Patella pellucida ORGANISM Patella pellucida Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Gastropoda; Patellogastropoda; Patelloidea; Patellidae; Patella. REFERENCE 1 (bases 1 to 1529) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (08-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Patella pellucida whole genome shotgun (WGS) project has the project accession CAKJPO000000000. This version of the project (01) has the accession number CAKJPO010000000, and consists of sequences CAKJPO010000001-CAKJPO010001529. The assembly xgPatPell1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 contains an large inversion between sister chromatids at approximately 15.43-87.97Mb. The inversion spans the majority of the chromosome 91.75Mb chromosome. FEATURES Location/Qualifiers source 1..1529 /organism="Patella pellucida" /mol_type="genomic DNA" /db_xref="taxon:88005" WGS CAKJPO010000001-CAKJPO010001529 // LOCUS CAKAVL010000000 371 rc DNA linear INV 11-OCT-2021 DEFINITION Erebia ligea, whole genome shotgun sequencing project. ACCESSION CAKAVL000000000 VERSION CAKAVL000000000.1 DBLINK BioProject: PRJEB47966 BioSample: SAMEA7523313 KEYWORDS WGS. SOURCE Erebia ligea (Arran brown butterfly) ORGANISM Erebia ligea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Satyrinae; Erebiini; Erebia. REFERENCE 1 (bases 1 to 371) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (07-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Erebia ligea whole genome shotgun (WGS) project has the project accession CAKAVL000000000. This version of the project (01) has the accession number CAKAVL010000000, and consists of sequences CAKAVL010000001-CAKAVL010000371. The assembly ilEreLige1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..371 /organism="Erebia ligea" /mol_type="genomic DNA" /db_xref="taxon:111903" WGS CAKAVL010000001-CAKAVL010000371 // LOCUS CAKJPM010000000 75 rc DNA linear INV 11-OCT-2021 DEFINITION Athalia rosae, whole genome shotgun sequencing project. ACCESSION CAKJPM000000000 VERSION CAKJPM000000000.1 DBLINK BioProject: PRJEB47994 BioSample: SAMEA7520481 Sequence Read Archive: ERR6054977, ERR6054978, ERR6054979, ERR6054980, ERR6054981, ERR6548410 KEYWORDS WGS. SOURCE Athalia rosae (coleseed sawfly) ORGANISM Athalia rosae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Tenthredinoidea; Tenthredinidae; Allantinae; Athalia. REFERENCE 1 (bases 1 to 75) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (08-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Athalia rosae whole genome shotgun (WGS) project has the project accession CAKJPM000000000. This version of the project (01) has the accession number CAKJPM010000000, and consists of sequences CAKJPM010000001-CAKJPM010000075. The assembly iyAthRosa1.1 is based on 103x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..75 /organism="Athalia rosae" /mol_type="genomic DNA" /db_xref="taxon:37344" WGS CAKJPM010000001-CAKJPM010000075 // LOCUS JAIZDN010000000 48 rc DNA linear VRT 13-OCT-2021 DEFINITION Scatophagus argus isolate fScaArg1, whole genome shotgun sequencing project. ACCESSION JAIZDN000000000 VERSION JAIZDN000000000.1 DBLINK BioProject: PRJNA749579 BioSample: SAMN12623616 KEYWORDS WGS. SOURCE Scatophagus argus ORGANISM Scatophagus argus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Scatophagidae; Scatophagus. REFERENCE 1 (bases 1 to 48) AUTHORS Myers,G., Pippel,M., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Bryappa,V., Jarvis,E.D. and Durbin,R. TITLE Scatophagus argus (Spotted scat) genome, fScaArg1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 48) AUTHORS Myers,G., Pippel,M., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Bryappa,V., Jarvis,E.D. and Durbin,R. TITLE Direct Submission JOURNAL Submitted (04-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Scatophagus argus whole genome shotgun (WGS) project has the project accession JAIZDN000000000. This version of the project (01) has the accession number JAIZDN010000000, and consists of sequences JAIZDN010000001-JAIZDN010000048. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: falcon-kit v. 1.3.0; FALCON-Unzip v. 1.2.0; purge_dups v. 1.2.3; scaff10X v. 4.2; bionano Solve v. Solve3.5_12162019; Salsa2 HiC v. 2.2; Longranger Align v. 2.2.2; pbmm2 v. 1.4.0; gcpp v. 1.0.0-1807624; bcftools v. 1.12-21-ga865a16; merfin v. 09c026d; deepvariant v. 1.1.0; gEVAL manual curation v. 2021-07-16 Assembly Name :: fScaArg1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 92.59x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..48 /organism="Scatophagus argus" /mol_type="genomic DNA" /isolate="fScaArg1" /db_xref="taxon:75038" /tissue_type="muscle" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-06" /collected_by="Byrappa Venkatesh" WGS JAIZDN010000001-JAIZDN010000048 WGS_SCAFLD CM035567-CM035590 WGS_SCAFLD CM035598 // LOCUS CAKJPN010000000 53 rc DNA linear INV 11-OCT-2021 DEFINITION Patella pellucida, whole genome shotgun sequencing project. ACCESSION CAKJPN000000000 VERSION CAKJPN000000000.1 DBLINK BioProject: PRJEB47996 BioSample: SAMEA7522851 Sequence Read Archive: ERR6054924, ERR6054925, ERR6054926, ERR6054927, ERR6054928, ERR6054929, ERR6412040 KEYWORDS WGS. SOURCE Patella pellucida ORGANISM Patella pellucida Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Gastropoda; Patellogastropoda; Patelloidea; Patellidae; Patella. REFERENCE 1 (bases 1 to 53) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (08-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Patella pellucida whole genome shotgun (WGS) project has the project accession CAKJPN000000000. This version of the project (01) has the accession number CAKJPN010000000, and consists of sequences CAKJPN010000001-CAKJPN010000053. The assembly xgPatPell1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 contains an large inversion between sister chromatids at approximately 15.43-87.97Mb. The inversion spans the majority of the chromosome 91.75Mb chromosome. FEATURES Location/Qualifiers source 1..53 /organism="Patella pellucida" /mol_type="genomic DNA" /db_xref="taxon:88005" WGS CAKJPN010000001-CAKJPN010000053 // LOCUS CAKJPL010000000 6 rc DNA linear INV 11-OCT-2021 DEFINITION Athalia rosae, whole genome shotgun sequencing project. ACCESSION CAKJPL000000000 VERSION CAKJPL000000000.1 DBLINK BioProject: PRJEB47993 BioSample: SAMEA7520481 Sequence Read Archive: ERR6054977, ERR6054978, ERR6054979, ERR6054980, ERR6054981, ERR6548410 KEYWORDS WGS. SOURCE Athalia rosae (coleseed sawfly) ORGANISM Athalia rosae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Tenthredinoidea; Tenthredinidae; Allantinae; Athalia. REFERENCE 1 (bases 1 to 6) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (08-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Athalia rosae whole genome shotgun (WGS) project has the project accession CAKJPL000000000. This version of the project (01) has the accession number CAKJPL010000000, and consists of sequences CAKJPL010000001-CAKJPL010000006. The assembly iyAthRosa1.1 is based on 103x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..6 /organism="Athalia rosae" /mol_type="genomic DNA" /db_xref="taxon:37344" WGS CAKJPL010000001-CAKJPL010000006 // LOCUS CAKAVA010000000 14 rc DNA linear INV 11-OCT-2021 DEFINITION Erebia ligea, whole genome shotgun sequencing project. ACCESSION CAKAVA000000000 VERSION CAKAVA000000000.1 DBLINK BioProject: PRJEB47965 BioSample: SAMEA7523313 KEYWORDS WGS. SOURCE Erebia ligea (Arran brown butterfly) ORGANISM Erebia ligea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Satyrinae; Erebiini; Erebia. REFERENCE 1 (bases 1 to 14) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (07-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Erebia ligea whole genome shotgun (WGS) project has the project accession CAKAVA000000000. This version of the project (01) has the accession number CAKAVA010000000, and consists of sequences CAKAVA010000001-CAKAVA010000014. The assembly ilEreLige1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..14 /organism="Erebia ligea" /mol_type="genomic DNA" /db_xref="taxon:111903" WGS CAKAVA010000001-CAKAVA010000014 // LOCUS CAKASR010000000 4 rc DNA linear INV 11-OCT-2021 DEFINITION Orgyia antiqua, whole genome shotgun sequencing project. ACCESSION CAKASR000000000 VERSION CAKASR000000000.1 DBLINK BioProject: PRJEB47958 BioSample: SAMEA7524390 KEYWORDS WGS. SOURCE Orgyia antiqua (rusty tussock moth) ORGANISM Orgyia antiqua Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Lymantriinae; Orgyia. REFERENCE 1 (bases 1 to 4) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (06-OCT-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Orgyia antiqua whole genome shotgun (WGS) project has the project accession CAKASR000000000. This version of the project (01) has the accession number CAKASR010000000, and consists of sequences CAKASR010000001-CAKASR010000004. The assembly ilOrgAnti1.1 is based on 14x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4 /organism="Orgyia antiqua" /mol_type="genomic DNA" /db_xref="taxon:335469" WGS CAKASR010000001-CAKASR010000004 // LOCUS JAIZDO010000000 1592 rc DNA linear VRT 07-OCT-2021 DEFINITION Scatophagus argus isolate fScaArg1, whole genome shotgun sequencing project. ACCESSION JAIZDO000000000 VERSION JAIZDO000000000.1 DBLINK BioProject: PRJNA749580 BioSample: SAMN12623616 KEYWORDS WGS. SOURCE Scatophagus argus ORGANISM Scatophagus argus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Scatophagidae; Scatophagus. REFERENCE 1 (bases 1 to 1592) AUTHORS Myers,G., Pippel,M., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Bryappa,V., Jarvis,E.D. and Durbin,R. TITLE Scatophagus argus (Spotted scat) genome, fScaArg1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1592) AUTHORS Myers,G., Pippel,M., Wrinkler,S., Tracey,A., Sims,Y., Wood,J., Fedrigo,O., Bryappa,V., Jarvis,E.D. and Durbin,R. TITLE Direct Submission JOURNAL Submitted (04-OCT-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Scatophagus argus whole genome shotgun (WGS) project has the project accession JAIZDO000000000. This version of the project (01) has the accession number JAIZDO010000000, and consists of sequences JAIZDO010000001-JAIZDO010001592. ##Genome-Assembly-Data-START## Assembly Date :: 16-JUL-2021 Assembly Method :: falcon-kit v. 1.3.0; FALCON-Unzip v. 1.2.0; purge_dups v. 1.2.3; scaff10X v. 4.2; bionano Solve Solve v. 3.5_12162019; Salsa2 HiC v. 2.2; Longranger Align v. 2.2.2; pbmm2 v. 1.4.0; gcpp v. 1.0.0-1807624; bcftools v. 1.12-21-ga865a16; merfin v. 09c026d; deepvariant v. 1.1.0; gEVAL manual curation v. 2021-07-16 Assembly Name :: fScaArg1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 92.59x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1592 /organism="Scatophagus argus" /mol_type="genomic DNA" /isolate="fScaArg1" /db_xref="taxon:75038" /tissue_type="muscle" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-06" /collected_by="Byrappa Venkatesh" WGS JAIZDO010000001-JAIZDO010001592 // LOCUS JAENSL010000000 685 rc DNA linear VRT 01-OCT-2021 DEFINITION Gallus gallus breed Cross of Broiler mother + white leghorn layer father isolate bGalGal1, whole genome shotgun sequencing project. ACCESSION JAENSL000000000 VERSION JAENSL000000000.1 DBLINK BioProject: PRJNA660758 BioSample: SAMN15960293 KEYWORDS WGS. SOURCE Gallus gallus (chicken) ORGANISM Gallus gallus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus. REFERENCE 1 (bases 1 to 685) AUTHORS Warren,W., Formenti,G., Fedrigo,O., Haase,B., Mountcastle,J., Balacco,J., Tracey,A., Schneider,V., Okimoto,R., Cheng,H., Hawken,R., Howe,K. and Jarvis,E.D. TITLE Gallus gallus (Chicken) genome, bGalGal1, GRCg7w, paternal haplotype autosomes JOURNAL Unpublished REFERENCE 2 (bases 1 to 685) AUTHORS Warren,W., Formenti,G., Fedrigo,O., Haase,B., Mountcastle,J., Balacco,J., Tracey,A., Schneider,V., Okimoto,R., Cheng,H., Hawken,R., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (14-NOV-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 685) AUTHORS Warren,W., Formenti,G., Fedrigo,O., Haase,B., Mountcastle,J., Balacco,J., Tracey,A., Schneider,V., Okimoto,R., Cheng,H., Hawken,R., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (04-SEP-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Oct 1, 2021 this sequence version replaced gi:1955616402. The Gallus gallus whole genome shotgun (WGS) project has the project accession JAENSL000000000. This version of the project (01) has the accession number JAENSL010000000, and consists of sequences JAENSL010000001-JAENSL010000685. Contigs JAENSL010000510-JAENSL010000685 were added to the assembly in September 2021. They are copies of the sequences of the sex chromosomes W and Z from the corresponding maternal haplotype assembly JAENSK000000000 (bGalGal1.mat.broiler.GRCg7b, GCA_016699485.1). Therefore, this updated assembly bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ (GCA_016700215.2) represents the male/paternal haplotype assembly plus the female/maternal haplotype assembly's sex chromosomes. ##Genome-Assembly-Data-START## Assembly Date :: 09-JUL-2020 Assembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. SMRTLink7.0.1; Freebayes v. 1.3.1; gEVAL manual curation v. 2020-07-09; VGP trio assembly pipeline v. 1.6 Assembly Name :: bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 102.01x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..685 /organism="Gallus gallus" /mol_type="genomic DNA" /isolate="bGalGal1" /db_xref="taxon:9031" /sex="female" /tissue_type="blood" /country="USA:Fayetteville, Arkansas" /lat_lon="36.0822 N 94.1719 W" /collection_date="20-May-2019" /collected_by="Nick Anthony" /note="breed: Cross of Broiler mother + white leghorn layer father" WGS JAENSL010000001-JAENSL010000685 WGS_SCAFLD CM028523-CM028561 WGS_SCAFLD CM035081-CM035082 WGS_SCAFLD MU179280-MU179296 WGS_SCAFLD MU255142-MU255145 // LOCUS CAKAJO010000000 2229 rc DNA linear INV 30-SEP-2021 DEFINITION Steromphala cineraria, whole genome shotgun sequencing project. ACCESSION CAKAJO000000000 VERSION CAKAJO000000000.1 DBLINK BioProject: PRJEB47763 BioSample: SAMEA7536348 KEYWORDS WGS. SOURCE Steromphala cineraria ORGANISM Steromphala cineraria Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Gastropoda; Vetigastropoda; Trochida; Trochoidea; Trochidae; Cantharidinae; Steromphala. REFERENCE 1 (bases 1 to 2229) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Steromphala cineraria whole genome shotgun (WGS) project has the project accession CAKAJO000000000. This version of the project (01) has the accession number CAKAJO010000000, and consists of sequences CAKAJO010000001-CAKAJO010002229. The assembly xgSteCine2.1 is based on 42x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Large inversions between sister chromatids can be seen on chromosome 5 29.7-60.7mb and chromosome 11 17.7-39.7mb. Possible inversions on chromosome 11 3.4-39.4 and 18-66mb. FEATURES Location/Qualifiers source 1..2229 /organism="Steromphala cineraria" /mol_type="genomic DNA" /db_xref="taxon:216125" WGS CAKAJO010000001-CAKAJO010002229 // LOCUS QXTK01000000 22244 rc DNA linear MAM 01-OCT-2021 DEFINITION Ursus arctos horribilis isolate GAN/ISIS:MIG12-29695490/34125, whole genome shotgun sequencing project. ACCESSION QXTK00000000 VERSION QXTK00000000.1 DBLINK BioProject: PRJNA487641 BioSample: SAMN09907428 KEYWORDS WGS. SOURCE Ursus arctos horribilis ORGANISM Ursus arctos horribilis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Ursidae; Ursus. REFERENCE 1 (bases 1 to 22244) AUTHORS Taylor,G.A., Kirk,H., Coombe,L., Jackman,S.D., Chu,J., Tse,K., Cheng,D., Chuah,E., Pandoh,P., Carlsen,R., Zhao,Y., Mungall,A.J., Moore,R., Birol,I., Franke,M., Marra,M.A., Dutton,C. and Jones,S.J.M. TITLE The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis JOURNAL Genes (Basel) 9 (12), E598 (2018) PUBMED 30513700 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 22244) AUTHORS Taylor,G.A., Kirk,H., Tse,K., Cheung,D., Chuah,E., Pandoh,P., Thorne,R., Zhao,Y., Mungall,A.J., Moore,R., Maria,F., Marra,M., Dutton,C. and Jones,S.J. TITLE Direct Submission JOURNAL Submitted (29-AUG-2018) Genome Sciences Centre, BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, 100-570 West 7th Ave, Vancouver, BC V5Z-4S6, Canada COMMENT The Ursus arctos horribilis whole genome shotgun (WGS) project has the project accession QXTK00000000. This version of the project (01) has the accession number QXTK01000000, and consists of sequences QXTK01000001-QXTK01022244. The mitochondrial genome record CM035080 was created in October 2021 when contig QXTK01022244 was recognized as being mitochondrial. This correction caused the assembly's accession to be updated to GCA_003584765.2. ##Genome-Assembly-Data-START## Assembly Date :: JUL-2018 Assembly Method :: Supernova v. 2.0.1 Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 50.0x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..22244 /organism="Ursus arctos horribilis" /mol_type="genomic DNA" /isolate="GAN/ISIS:MIG12-29695490/34125" /sub_species="horribilis" /db_xref="taxon:116960" /sex="male" /tissue_type="blood" /dev_stage="adult" WGS QXTK01000001-QXTK01022244 WGS_SCAFLD CM035080 WGS_SCAFLD KZ986268-KZ987398 // LOCUS CAKAJM010000000 1136 rc DNA linear INV 30-SEP-2021 DEFINITION Mesoligia furuncula, whole genome shotgun sequencing project. ACCESSION CAKAJM000000000 VERSION CAKAJM000000000.1 DBLINK BioProject: PRJEB47755 BioSample: SAMEA7701289 KEYWORDS WGS. SOURCE Mesoligia furuncula ORGANISM Mesoligia furuncula Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Mesoligia. REFERENCE 1 (bases 1 to 1136) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mesoligia furuncula whole genome shotgun (WGS) project has the project accession CAKAJM000000000. This version of the project (01) has the accession number CAKAJM010000000, and consists of sequences CAKAJM010000001-CAKAJM010001136. The assembly ilMesFuru1.1 is based on 24x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Linkage has been observed in the Hi-C map between chromosomes 8 and 25. This linkage is specific, such that an alternative karyotype could be constructed {8A:8B,25A:25B} and {8B:25A,8A,25B}. No support for this fusion between chromosome 8 and 25 can be seen in the PacBio reads which derive from a different sample to the Hi-C. FEATURES Location/Qualifiers source 1..1136 /organism="Mesoligia furuncula" /mol_type="genomic DNA" /db_xref="taxon:997551" WGS CAKAJM010000001-CAKAJM010001136 // LOCUS CAKAJV010000000 301 rc DNA linear INV 30-SEP-2021 DEFINITION Xestia c-nigrum, whole genome shotgun sequencing project. ACCESSION CAKAJV000000000 VERSION CAKAJV000000000.1 DBLINK BioProject: PRJEB47752 BioSample: SAMEA8239458 KEYWORDS WGS. SOURCE Xestia c-nigrum (spotted cutworm) ORGANISM Xestia c-nigrum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Xestia. REFERENCE 1 (bases 1 to 301) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Xestia c-nigrum whole genome shotgun (WGS) project has the project accession CAKAJV000000000. This version of the project (01) has the accession number CAKAJV010000000, and consists of sequences CAKAJV010000001-CAKAJV010000301. The assembly ilXesCnig1.1 is based on 35x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..301 /organism="Xestia c-nigrum" /mol_type="genomic DNA" /db_xref="taxon:987431" WGS CAKAJV010000001-CAKAJV010000301 // LOCUS CAKAJD010000000 2093 rc DNA linear INV 30-SEP-2021 DEFINITION Gymnosoma rotundatum, whole genome shotgun sequencing project. ACCESSION CAKAJD000000000 VERSION CAKAJD000000000.1 DBLINK BioProject: PRJEB47733 BioSample: SAMEA7849381 KEYWORDS WGS. SOURCE Gymnosoma rotundatum ORGANISM Gymnosoma rotundatum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Tachinidae; Phasiinae; Gymnosomatini; Gymnosoma. REFERENCE 1 (bases 1 to 2093) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Gymnosoma rotundatum whole genome shotgun (WGS) project has the project accession CAKAJD000000000. This version of the project (01) has the accession number CAKAJD010000000, and consists of sequences CAKAJD010000001-CAKAJD010002093. The assembly idGymRotn1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The X chromosome has been identified based on half diploid coverage. There are a large amount of spare scaffolds which may be X or may be Y as we are uncertain whether the karyotype is XO or XY. FEATURES Location/Qualifiers source 1..2093 /organism="Gymnosoma rotundatum" /mol_type="genomic DNA" /db_xref="taxon:569046" WGS CAKAJD010000001-CAKAJD010002093 // LOCUS CAKAJF010000000 2490 rc DNA linear INV 30-SEP-2021 DEFINITION Griposia aprilina, whole genome shotgun sequencing project. ACCESSION CAKAJF000000000 VERSION CAKAJF000000000.1 DBLINK BioProject: PRJEB47742 BioSample: SAMEA8603200 KEYWORDS WGS. SOURCE Griposia aprilina ORGANISM Griposia aprilina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Griposia. REFERENCE 1 (bases 1 to 2490) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Griposia aprilina whole genome shotgun (WGS) project has the project accession CAKAJF000000000. This version of the project (01) has the accession number CAKAJF010000000, and consists of sequences CAKAJF010000001-CAKAJF010002490. The assembly ilGriApri1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2490 /organism="Griposia aprilina" /mol_type="genomic DNA" /db_xref="taxon:1101106" WGS CAKAJF010000001-CAKAJF010002490 // LOCUS CAKAIW010000000 1694 rc DNA linear INV 30-SEP-2021 DEFINITION Omphaloscelis lunosa, whole genome shotgun sequencing project. ACCESSION CAKAIW000000000 VERSION CAKAIW000000000.1 DBLINK BioProject: PRJEB47744 BioSample: SAMEA8603195 KEYWORDS WGS. SOURCE Omphaloscelis lunosa ORGANISM Omphaloscelis lunosa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Omphaloscelis. REFERENCE 1 (bases 1 to 1694) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Omphaloscelis lunosa whole genome shotgun (WGS) project has the project accession CAKAIW000000000. This version of the project (01) has the accession number CAKAIW010000000, and consists of sequences CAKAIW010000001-CAKAIW010001694. The assembly ilOmpLuno1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. W chromosome identified based on approximately half diploid coverage level in some parts, and based on grouping by Hi-C data. The named W-scaffolds appear very repetitive as we would expect and therefore have an erratic coverage profile. Attempts to confirm as W via sequence homology with other lepidoptera were unsuccessful. 2 of the largest unassigned scaffolds place equally well on the ends of chromosome 27 and chromosome 28. FEATURES Location/Qualifiers source 1..1694 /organism="Omphaloscelis lunosa" /mol_type="genomic DNA" /db_xref="taxon:2492375" WGS CAKAIW010000001-CAKAIW010001694 // LOCUS CAKAJQ010000000 765 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJQ000000000 VERSION CAKAJQ000000000.1 DBLINK BioProject: PRJEB47760 BioSample: SAMEA9239977 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 765) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJQ000000000. This version of the project (01) has the accession number CAKAJQ010000000, and consists of sequences CAKAJQ010000001-CAKAJQ010000765. The assembly drMalDome58.1 is based on 24x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Inversions between haplotypes observed in chromosomes 1 5.49-7.32mb, 11 31.38-33.79mb, 12 10.26-14.45mb, 13 34.66-35.91mb and 17 22.1-25.48mb. FEATURES Location/Qualifiers source 1..765 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJQ010000001-CAKAJQ010000765 // LOCUS CAKAJP010000000 434 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJP000000000 VERSION CAKAJP000000000.1 DBLINK BioProject: PRJEB47757 BioSample: SAMEA9197674 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 434) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJP000000000. This version of the project (01) has the accession number CAKAJP010000000, and consists of sequences CAKAJP010000001-CAKAJP010000434. The assembly drMalDome11.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654. Evidence of inversions between haplotypes from the Hi-C map in chromosome 1 1.28-7.73mb and chromosome 5 14.88-16.83mb. FEATURES Location/Qualifiers source 1..434 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJP010000001-CAKAJP010000434 // LOCUS CAKAJS010000000 873 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJS000000000 VERSION CAKAJS000000000.1 DBLINK BioProject: PRJEB47759 BioSample: SAMEA8717325 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 873) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJS000000000. This version of the project (01) has the accession number CAKAJS010000000, and consists of sequences CAKAJS010000001-CAKAJS010000873. The assembly drMalDome5.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. From the Hi-C data, inversions between haplotypes can be seen on chromosome 4 11.13-14.86mb, chromosome 6 13.34-17.21mb, chromosome 11 22.9-24.24mb and 30.06-32.57mb, chromosome 12 10.9-11.98mb, chromosome 13 34-37mb. FEATURES Location/Qualifiers source 1..873 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJS010000001-CAKAJS010000873 // LOCUS CAKAJG010000000 3090 rc DNA linear INV 30-SEP-2021 DEFINITION Eristalis arbustorum, whole genome shotgun sequencing project. ACCESSION CAKAJG000000000 VERSION CAKAJG000000000.1 DBLINK BioProject: PRJEB47735 BioSample: SAMEA7520036 KEYWORDS WGS. SOURCE Eristalis arbustorum ORGANISM Eristalis arbustorum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Eristalini; Eristalis. REFERENCE 1 (bases 1 to 3090) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eristalis arbustorum whole genome shotgun (WGS) project has the project accession CAKAJG000000000. This version of the project (01) has the accession number CAKAJG010000000, and consists of sequences CAKAJG010000001-CAKAJG010003090. The assembly idEriArbu1.1 is based on 19x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Based on published karyotype potential micro-chromosomes have not been recovered in the curated assembly (Rozek,M et al (1995) Folia Biologica. C-banding patterns in chromosome of four species of syrphid flies (Diptera, Syrphidae)). FEATURES Location/Qualifiers source 1..3090 /organism="Eristalis arbustorum" /mol_type="genomic DNA" /db_xref="taxon:1124515" WGS CAKAJG010000001-CAKAJG010003090 // LOCUS CAKAJC010000000 1444 rc DNA linear INV 30-SEP-2021 DEFINITION Lasioglossum lativentre, whole genome shotgun sequencing project. ACCESSION CAKAJC000000000 VERSION CAKAJC000000000.1 DBLINK BioProject: PRJEB47728 BioSample: SAMEA7746765 KEYWORDS WGS. SOURCE Lasioglossum lativentre ORGANISM Lasioglossum lativentre Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Lasioglossum; Lasioglossum. REFERENCE 1 (bases 1 to 1444) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lasioglossum lativentre whole genome shotgun (WGS) project has the project accession CAKAJC000000000. This version of the project (01) has the accession number CAKAJC010000000, and consists of sequences CAKAJC010000001-CAKAJC010001444. The assembly iyLasLatv2.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1444 /organism="Lasioglossum lativentre" /mol_type="genomic DNA" /db_xref="taxon:88531" WGS CAKAJC010000001-CAKAJC010001444 // LOCUS CAKAIY010000000 590 rc DNA linear INV 30-SEP-2021 DEFINITION Lasioglossum morio, whole genome shotgun sequencing project. ACCESSION CAKAIY000000000 VERSION CAKAIY000000000.1 DBLINK BioProject: PRJEB47730 BioSample: SAMEA7746456 KEYWORDS WGS. SOURCE Lasioglossum morio ORGANISM Lasioglossum morio Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Lasioglossum; Dialictus. REFERENCE 1 (bases 1 to 590) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lasioglossum morio whole genome shotgun (WGS) project has the project accession CAKAIY000000000. This version of the project (01) has the accession number CAKAIY010000000, and consists of sequences CAKAIY010000001-CAKAIY010000590. The assembly iyLasMori1.1 is based on 35x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Several repeat types can be seen to cluster by Hi-C yet have no association with the defined chromosomes. These repeats make up a large proportion of the assembly. FEATURES Location/Qualifiers source 1..590 /organism="Lasioglossum morio" /mol_type="genomic DNA" /db_xref="taxon:88514" WGS CAKAIY010000001-CAKAIY010000590 // LOCUS CAKAIX010000000 774 rc DNA linear INV 30-SEP-2021 DEFINITION Cheilosia vulpina, whole genome shotgun sequencing project. ACCESSION CAKAIX000000000 VERSION CAKAIX000000000.1 DBLINK BioProject: PRJEB47737 BioSample: SAMEA7746587 KEYWORDS WGS. SOURCE Cheilosia vulpina ORGANISM Cheilosia vulpina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Rhingiini; Cheilosia. REFERENCE 1 (bases 1 to 774) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cheilosia vulpina whole genome shotgun (WGS) project has the project accession CAKAIX000000000. This version of the project (01) has the accession number CAKAIX010000000, and consists of sequences CAKAIX010000001-CAKAIX010000774. The assembly idCheVulp2.1 is based on 51x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..774 /organism="Cheilosia vulpina" /mol_type="genomic DNA" /db_xref="taxon:273409" WGS CAKAIX010000001-CAKAIX010000774 // LOCUS CAKAJJ010000000 860 rc DNA linear INV 30-SEP-2021 DEFINITION Haliclystus octoradiatus, whole genome shotgun sequencing project. ACCESSION CAKAJJ000000000 VERSION CAKAJJ000000000.1 DBLINK BioProject: PRJEB47764 BioSample: SAMEA7522858 KEYWORDS WGS. SOURCE Haliclystus octoradiatus ORGANISM Haliclystus octoradiatus Eukaryota; Metazoa; Cnidaria; Staurozoa; Stauromedusae; Myostaurida; Haliclystidae; Haliclystus. REFERENCE 1 (bases 1 to 860) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Haliclystus octoradiatus whole genome shotgun (WGS) project has the project accession CAKAJJ000000000. This version of the project (01) has the accession number CAKAJJ010000000, and consists of sequences CAKAJJ010000001-CAKAJJ010000860. The assembly jrHalOcto1.1 is based on 68x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..860 /organism="Haliclystus octoradiatus" /mol_type="genomic DNA" /db_xref="taxon:313498" WGS CAKAJJ010000001-CAKAJJ010000860 // LOCUS CAKAJX010000000 205 rc DNA linear INV 30-SEP-2021 DEFINITION Emmelina monodactyla, whole genome shotgun sequencing project. ACCESSION CAKAJX000000000 VERSION CAKAJX000000000.1 DBLINK BioProject: PRJEB47748 BioSample: SAMEA8603203 KEYWORDS WGS. SOURCE Emmelina monodactyla (morning-glory plume moth) ORGANISM Emmelina monodactyla Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pterophoroidea; Pterophoridae; Pterophorinae; Emmelina. REFERENCE 1 (bases 1 to 205) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Emmelina monodactyla whole genome shotgun (WGS) project has the project accession CAKAJX000000000. This version of the project (01) has the accession number CAKAJX010000000, and consists of sequences CAKAJX010000001-CAKAJX010000205. The assembly ilEmmMono1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..205 /organism="Emmelina monodactyla" /mol_type="genomic DNA" /db_xref="taxon:467774" WGS CAKAJX010000001-CAKAJX010000205 // LOCUS CAKAJE010000000 2141 rc DNA linear INV 30-SEP-2021 DEFINITION Macropis europaea, whole genome shotgun sequencing project. ACCESSION CAKAJE000000000 VERSION CAKAJE000000000.1 DBLINK BioProject: PRJEB47740 BioSample: SAMEA7746440 KEYWORDS WGS. SOURCE Macropis europaea ORGANISM Macropis europaea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Melittinae; Macropis. REFERENCE 1 (bases 1 to 2141) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Macropis europaea whole genome shotgun (WGS) project has the project accession CAKAJE000000000. This version of the project (01) has the accession number CAKAJE010000000, and consists of sequences CAKAJE010000001-CAKAJE010002141. The assembly iyMacEuro1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. We see an unusually large proportion of satellite repeat in this assembly which is unplaceable using the Hi-C map. FEATURES Location/Qualifiers source 1..2141 /organism="Macropis europaea" /mol_type="genomic DNA" /db_xref="taxon:253715" WGS CAKAJE010000001-CAKAJE010002141 // LOCUS CAKAJA010000000 542 rc DNA linear INV 30-SEP-2021 DEFINITION Lasioglossum morio, whole genome shotgun sequencing project. ACCESSION CAKAJA000000000 VERSION CAKAJA000000000.1 DBLINK BioProject: PRJEB47731 BioSample: SAMEA7746456 KEYWORDS WGS. SOURCE Lasioglossum morio ORGANISM Lasioglossum morio Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Lasioglossum; Dialictus. REFERENCE 1 (bases 1 to 542) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lasioglossum morio whole genome shotgun (WGS) project has the project accession CAKAJA000000000. This version of the project (01) has the accession number CAKAJA010000000, and consists of sequences CAKAJA010000001-CAKAJA010000542. The assembly iyLasMori1.1 is based on 35x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Several repeat types can be seen to cluster by Hi-C yet have no association with the defined chromosomes. These repeats make up a large proportion of the assembly. FEATURES Location/Qualifiers source 1..542 /organism="Lasioglossum morio" /mol_type="genomic DNA" /db_xref="taxon:88514" WGS CAKAJA010000001-CAKAJA010000542 // LOCUS CAKAJI010000000 1129 rc DNA linear INV 30-SEP-2021 DEFINITION Lasioglossum lativentre, whole genome shotgun sequencing project. ACCESSION CAKAJI000000000 VERSION CAKAJI000000000.1 DBLINK BioProject: PRJEB47729 BioSample: SAMEA7746765 KEYWORDS WGS. SOURCE Lasioglossum lativentre ORGANISM Lasioglossum lativentre Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Halictidae; Halictinae; Halictini; Lasioglossum; Lasioglossum. REFERENCE 1 (bases 1 to 1129) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lasioglossum lativentre whole genome shotgun (WGS) project has the project accession CAKAJI000000000. This version of the project (01) has the accession number CAKAJI010000000, and consists of sequences CAKAJI010000001-CAKAJI010001129. The assembly iyLasLatv2.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1129 /organism="Lasioglossum lativentre" /mol_type="genomic DNA" /db_xref="taxon:88531" WGS CAKAJI010000001-CAKAJI010001129 // LOCUS CAKAJB010000000 421 rc DNA linear INV 30-SEP-2021 DEFINITION Gymnosoma rotundatum, whole genome shotgun sequencing project. ACCESSION CAKAJB000000000 VERSION CAKAJB000000000.1 DBLINK BioProject: PRJEB47732 BioSample: SAMEA7849381 KEYWORDS WGS. SOURCE Gymnosoma rotundatum ORGANISM Gymnosoma rotundatum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Tachinidae; Phasiinae; Gymnosomatini; Gymnosoma. REFERENCE 1 (bases 1 to 421) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Gymnosoma rotundatum whole genome shotgun (WGS) project has the project accession CAKAJB000000000. This version of the project (01) has the accession number CAKAJB010000000, and consists of sequences CAKAJB010000001-CAKAJB010000421. The assembly idGymRotn1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The X chromosome has been identified based on half diploid coverage. There are a large amount of spare scaffolds which may be X or may be Y as we are uncertain whether the karyotype is XO or XY. FEATURES Location/Qualifiers source 1..421 /organism="Gymnosoma rotundatum" /mol_type="genomic DNA" /db_xref="taxon:569046" WGS CAKAJB010000001-CAKAJB010000421 // LOCUS CAKAIZ010000000 512 rc DNA linear INV 30-SEP-2021 DEFINITION Eristalis arbustorum, whole genome shotgun sequencing project. ACCESSION CAKAIZ000000000 VERSION CAKAIZ000000000.1 DBLINK BioProject: PRJEB47734 BioSample: SAMEA7520036 KEYWORDS WGS. SOURCE Eristalis arbustorum ORGANISM Eristalis arbustorum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Eristalini; Eristalis. REFERENCE 1 (bases 1 to 512) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eristalis arbustorum whole genome shotgun (WGS) project has the project accession CAKAIZ000000000. This version of the project (01) has the accession number CAKAIZ010000000, and consists of sequences CAKAIZ010000001-CAKAIZ010000512. The assembly idEriArbu1.1 is based on 19x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Based on published karyotype potential micro-chromosomes have not been recovered in the curated assembly (Rozek,M et al (1995) Folia Biologica. C-banding patterns in chromosome of four species of syrphid flies (Diptera, Syrphidae)). FEATURES Location/Qualifiers source 1..512 /organism="Eristalis arbustorum" /mol_type="genomic DNA" /db_xref="taxon:1124515" WGS CAKAIZ010000001-CAKAIZ010000512 // LOCUS CAKAJN010000000 265 rc DNA linear INV 30-SEP-2021 DEFINITION Steromphala cineraria, whole genome shotgun sequencing project. ACCESSION CAKAJN000000000 VERSION CAKAJN000000000.1 DBLINK BioProject: PRJEB47762 BioSample: SAMEA7536348 KEYWORDS WGS. SOURCE Steromphala cineraria ORGANISM Steromphala cineraria Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Gastropoda; Vetigastropoda; Trochida; Trochoidea; Trochidae; Cantharidinae; Steromphala. REFERENCE 1 (bases 1 to 265) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Steromphala cineraria whole genome shotgun (WGS) project has the project accession CAKAJN000000000. This version of the project (01) has the accession number CAKAJN010000000, and consists of sequences CAKAJN010000001-CAKAJN010000265. The assembly xgSteCine2.1 is based on 42x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Large inversions between sister chromatids can be seen on chromosome 5 29.7-60.7mb and chromosome 11 17.7-39.7mb. Possible inversions on chromosome 11 3.4-39.4 and 18-66mb. FEATURES Location/Qualifiers source 1..265 /organism="Steromphala cineraria" /mol_type="genomic DNA" /db_xref="taxon:216125" WGS CAKAJN010000001-CAKAJN010000265 // LOCUS CAKAIT010000000 17 rc DNA linear INV 30-SEP-2021 DEFINITION Omphaloscelis lunosa, whole genome shotgun sequencing project. ACCESSION CAKAIT000000000 VERSION CAKAIT000000000.1 DBLINK BioProject: PRJEB47743 BioSample: SAMEA8603195 KEYWORDS WGS. SOURCE Omphaloscelis lunosa ORGANISM Omphaloscelis lunosa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Omphaloscelis. REFERENCE 1 (bases 1 to 17) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Omphaloscelis lunosa whole genome shotgun (WGS) project has the project accession CAKAIT000000000. This version of the project (01) has the accession number CAKAIT010000000, and consists of sequences CAKAIT010000001-CAKAIT010000017. The assembly ilOmpLuno1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. W chromosome identified based on approximately half diploid coverage level in some parts, and based on grouping by Hi-C data. The named W-scaffolds appear very repetitive as we would expect and therefore have an erratic coverage profile. Attempts to confirm as W via sequence homology with other lepidoptera were unsuccessful. 2 of the largest unassigned scaffolds place equally well on the ends of chromosome 27 and chromosome 28. FEATURES Location/Qualifiers source 1..17 /organism="Omphaloscelis lunosa" /mol_type="genomic DNA" /db_xref="taxon:2492375" WGS CAKAIT010000001-CAKAIT010000017 // LOCUS CAKAJH010000000 121 rc DNA linear INV 30-SEP-2021 DEFINITION Macropis europaea, whole genome shotgun sequencing project. ACCESSION CAKAJH000000000 VERSION CAKAJH000000000.1 DBLINK BioProject: PRJEB47739 BioSample: SAMEA7746440 KEYWORDS WGS. SOURCE Macropis europaea ORGANISM Macropis europaea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Melittinae; Macropis. REFERENCE 1 (bases 1 to 121) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Macropis europaea whole genome shotgun (WGS) project has the project accession CAKAJH000000000. This version of the project (01) has the accession number CAKAJH010000000, and consists of sequences CAKAJH010000001-CAKAJH010000121. The assembly iyMacEuro1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. We see an unusually large proportion of satellite repeat in this assembly which is unplaceable using the Hi-C map. FEATURES Location/Qualifiers source 1..121 /organism="Macropis europaea" /mol_type="genomic DNA" /db_xref="taxon:253715" WGS CAKAJH010000001-CAKAJH010000121 // LOCUS CAKAJU010000000 44 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJU000000000 VERSION CAKAJU000000000.1 DBLINK BioProject: PRJEB47761 BioSample: SAMEA9239977 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 44) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJU000000000. This version of the project (01) has the accession number CAKAJU010000000, and consists of sequences CAKAJU010000001-CAKAJU010000044. The assembly drMalDome58.1 is based on 24x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Inversions between haplotypes observed in chromosomes 1 5.49-7.32mb, 11 31.38-33.79mb, 12 10.26-14.45mb, 13 34.66-35.91mb and 17 22.1-25.48mb. FEATURES Location/Qualifiers source 1..44 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJU010000001-CAKAJU010000044 // LOCUS CAKAIV010000000 10 rc DNA linear INV 30-SEP-2021 DEFINITION Griposia aprilina, whole genome shotgun sequencing project. ACCESSION CAKAIV000000000 VERSION CAKAIV000000000.1 DBLINK BioProject: PRJEB47741 BioSample: SAMEA8603200 KEYWORDS WGS. SOURCE Griposia aprilina ORGANISM Griposia aprilina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Griposia. REFERENCE 1 (bases 1 to 10) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Griposia aprilina whole genome shotgun (WGS) project has the project accession CAKAIV000000000. This version of the project (01) has the accession number CAKAIV010000000, and consists of sequences CAKAIV010000001-CAKAIV010000010. The assembly ilGriApri1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..10 /organism="Griposia aprilina" /mol_type="genomic DNA" /db_xref="taxon:1101106" WGS CAKAIV010000001-CAKAIV010000010 // LOCUS CAKAJR010000000 62 rc DNA linear INV 30-SEP-2021 DEFINITION Mesoligia furuncula, whole genome shotgun sequencing project. ACCESSION CAKAJR000000000 VERSION CAKAJR000000000.1 DBLINK BioProject: PRJEB47754 BioSample: SAMEA7701289 KEYWORDS WGS. SOURCE Mesoligia furuncula ORGANISM Mesoligia furuncula Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Mesoligia. REFERENCE 1 (bases 1 to 62) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mesoligia furuncula whole genome shotgun (WGS) project has the project accession CAKAJR000000000. This version of the project (01) has the accession number CAKAJR010000000, and consists of sequences CAKAJR010000001-CAKAJR010000062. The assembly ilMesFuru1.1 is based on 24x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Linkage has been observed in the Hi-C map between chromosomes 8 and 25. This linkage is specific, such that an alternative karyotype could be constructed {8A:8B,25A:25B} and {8B:25A,8A,25B}. No support for this fusion between chromosome 8 and 25 can be seen in the PacBio reads which derive from a different sample to the Hi-C. FEATURES Location/Qualifiers source 1..62 /organism="Mesoligia furuncula" /mol_type="genomic DNA" /db_xref="taxon:997551" WGS CAKAJR010000001-CAKAJR010000062 // LOCUS CAKAJK010000000 24 rc DNA linear INV 30-SEP-2021 DEFINITION Haliclystus octoradiatus, whole genome shotgun sequencing project. ACCESSION CAKAJK000000000 VERSION CAKAJK000000000.1 DBLINK BioProject: PRJEB47765 BioSample: SAMEA7522858 KEYWORDS WGS. SOURCE Haliclystus octoradiatus ORGANISM Haliclystus octoradiatus Eukaryota; Metazoa; Cnidaria; Staurozoa; Stauromedusae; Myostaurida; Haliclystidae; Haliclystus. REFERENCE 1 (bases 1 to 24) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Haliclystus octoradiatus whole genome shotgun (WGS) project has the project accession CAKAJK000000000. This version of the project (01) has the accession number CAKAJK010000000, and consists of sequences CAKAJK010000001-CAKAJK010000024. The assembly jrHalOcto1.1 is based on 68x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..24 /organism="Haliclystus octoradiatus" /mol_type="genomic DNA" /db_xref="taxon:313498" WGS CAKAJK010000001-CAKAJK010000024 // LOCUS CAKAJL010000000 12 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJL000000000 VERSION CAKAJL000000000.1 DBLINK BioProject: PRJEB47756 BioSample: SAMEA9197674 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 12) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJL000000000. This version of the project (01) has the accession number CAKAJL010000000, and consists of sequences CAKAJL010000001-CAKAJL010000012. The assembly drMalDome11.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654. Evidence of inversions between haplotypes from the Hi-C map in chromosome 1 1.28-7.73mb and chromosome 5 14.88-16.83mb. FEATURES Location/Qualifiers source 1..12 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJL010000001-CAKAJL010000012 // LOCUS CAKAJT010000000 9 rc DNA linear PLN 30-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAKAJT000000000 VERSION CAKAJT000000000.1 DBLINK BioProject: PRJEB47758 BioSample: SAMEA8717325 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAKAJT000000000. This version of the project (01) has the accession number CAKAJT010000000, and consists of sequences CAKAJT010000001-CAKAJT010000009. The assembly drMalDome5.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. From the Hi-C data, inversions between haplotypes can be seen on chromosome 4 11.13-14.86mb, chromosome 6 13.34-17.21mb, chromosome 11 22.9-24.24mb and 30.06-32.57mb, chromosome 12 10.9-11.98mb, chromosome 13 34-37mb. FEATURES Location/Qualifiers source 1..9 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAKAJT010000001-CAKAJT010000009 // LOCUS CAKAJW010000000 12 rc DNA linear INV 30-SEP-2021 DEFINITION Xestia c-nigrum, whole genome shotgun sequencing project. ACCESSION CAKAJW000000000 VERSION CAKAJW000000000.1 DBLINK BioProject: PRJEB47753 BioSample: SAMEA8239458 KEYWORDS WGS. SOURCE Xestia c-nigrum (spotted cutworm) ORGANISM Xestia c-nigrum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Xestia. REFERENCE 1 (bases 1 to 12) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Xestia c-nigrum whole genome shotgun (WGS) project has the project accession CAKAJW000000000. This version of the project (01) has the accession number CAKAJW010000000, and consists of sequences CAKAJW010000001-CAKAJW010000012. The assembly ilXesCnig1.1 is based on 35x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..12 /organism="Xestia c-nigrum" /mol_type="genomic DNA" /db_xref="taxon:987431" WGS CAKAJW010000001-CAKAJW010000012 // LOCUS CAKAIU010000000 14 rc DNA linear INV 30-SEP-2021 DEFINITION Cheilosia vulpina, whole genome shotgun sequencing project. ACCESSION CAKAIU000000000 VERSION CAKAIU000000000.1 DBLINK BioProject: PRJEB47738 BioSample: SAMEA7746587 KEYWORDS WGS. SOURCE Cheilosia vulpina ORGANISM Cheilosia vulpina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Rhingiini; Cheilosia. REFERENCE 1 (bases 1 to 14) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cheilosia vulpina whole genome shotgun (WGS) project has the project accession CAKAIU000000000. This version of the project (01) has the accession number CAKAIU010000000, and consists of sequences CAKAIU010000001-CAKAIU010000014. The assembly idCheVulp2.1 is based on 51x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..14 /organism="Cheilosia vulpina" /mol_type="genomic DNA" /db_xref="taxon:273409" WGS CAKAIU010000001-CAKAIU010000014 // LOCUS CAKAJY010000000 4 rc DNA linear INV 30-SEP-2021 DEFINITION Emmelina monodactyla, whole genome shotgun sequencing project. ACCESSION CAKAJY000000000 VERSION CAKAJY000000000.1 DBLINK BioProject: PRJEB47749 BioSample: SAMEA8603203 KEYWORDS WGS. SOURCE Emmelina monodactyla (morning-glory plume moth) ORGANISM Emmelina monodactyla Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pterophoroidea; Pterophoridae; Pterophorinae; Emmelina. REFERENCE 1 (bases 1 to 4) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Emmelina monodactyla whole genome shotgun (WGS) project has the project accession CAKAJY000000000. This version of the project (01) has the accession number CAKAJY010000000, and consists of sequences CAKAJY010000001-CAKAJY010000004. The assembly ilEmmMono1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4 /organism="Emmelina monodactyla" /mol_type="genomic DNA" /db_xref="taxon:467774" WGS CAKAJY010000001-CAKAJY010000004 // LOCUS CAJZCT010000000 659 rc DNA linear INV 24-SEP-2021 DEFINITION Eilema sororculum, whole genome shotgun sequencing project. ACCESSION CAJZCT000000000 VERSION CAJZCT000000000.1 DBLINK BioProject: PRJEB47352 BioSample: SAMEA7631555 KEYWORDS WGS. SOURCE Eilema sororculum ORGANISM Eilema sororculum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Arctiinae; Eilema. REFERENCE 1 (bases 1 to 659) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (06-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eilema sororculum whole genome shotgun (WGS) project has the project accession CAJZCT000000000. This version of the project (01) has the accession number CAJZCT010000000, and consists of sequences CAJZCT010000001-CAJZCT010000659. The assembly ilEilSoro1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..659 /organism="Eilema sororculum" /mol_type="genomic DNA" /db_xref="taxon:987424" WGS CAJZCT010000001-CAJZCT010000659 // LOCUS CAJHWU020000000 252 rc DNA linear INV 24-SEP-2021 DEFINITION Vanessa atalanta, whole genome shotgun sequencing project. ACCESSION CAJHWU000000000 VERSION CAJHWU000000000.2 DBLINK BioProject: PRJEB41955 BioSample: SAMEA7523145 KEYWORDS WGS. SOURCE Vanessa atalanta (red admiral) ORGANISM Vanessa atalanta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Nymphalinae; Vanessa. REFERENCE 1 (bases 1 to 252) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 252) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (09-SEP-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Sep 28, 2021 this sequence version replaced CAJHWU000000000.1. The Vanessa atalanta whole genome shotgun (WGS) project has the project accession CAJHWU000000000. This version of the project (02) has the accession number CAJHWU020000000, and consists of sequences CAJHWU020000001-CAJHWU020000252. The assembly ilVanAtal1.2 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..252 /organism="Vanessa atalanta" /mol_type="genomic DNA" /db_xref="taxon:42275" WGS CAJHWU020000001-CAJHWU020000252 // LOCUS CAJHWX020000000 109 rc DNA linear INV 24-SEP-2021 DEFINITION Vanessa atalanta, whole genome shotgun sequencing project. ACCESSION CAJHWX000000000 VERSION CAJHWX000000000.2 DBLINK BioProject: PRJEB41956 BioSample: SAMEA7523145 KEYWORDS WGS. SOURCE Vanessa atalanta (red admiral) ORGANISM Vanessa atalanta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Nymphalinae; Vanessa. REFERENCE 1 (bases 1 to 109) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 109) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (09-SEP-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Sep 28, 2021 this sequence version replaced CAJHWX000000000.1. The Vanessa atalanta whole genome shotgun (WGS) project has the project accession CAJHWX000000000. This version of the project (02) has the accession number CAJHWX020000000, and consists of sequences CAJHWX020000001-CAJHWX020000109. The assembly ilVanAtal1.2 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..109 /organism="Vanessa atalanta" /mol_type="genomic DNA" /db_xref="taxon:42275" WGS CAJHWX020000001-CAJHWX020000109 // LOCUS CAJZCU010000000 10 rc DNA linear INV 24-SEP-2021 DEFINITION Eilema sororculum, whole genome shotgun sequencing project. ACCESSION CAJZCU000000000 VERSION CAJZCU000000000.1 DBLINK BioProject: PRJEB47353 BioSample: SAMEA7631555 KEYWORDS WGS. SOURCE Eilema sororculum ORGANISM Eilema sororculum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Arctiinae; Eilema. REFERENCE 1 (bases 1 to 10) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (06-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eilema sororculum whole genome shotgun (WGS) project has the project accession CAJZCU000000000. This version of the project (01) has the accession number CAJZCU010000000, and consists of sequences CAJZCU010000001-CAJZCU010000010. The assembly ilEilSoro1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..10 /organism="Eilema sororculum" /mol_type="genomic DNA" /db_xref="taxon:987424" WGS CAJZCU010000001-CAJZCU010000010 // LOCUS CAJVDD010000000 895 rc DNA linear VRT 21-SEP-2021 DEFINITION Thunnus maccoyii, whole genome shotgun sequencing project. ACCESSION CAJVDD000000000 VERSION CAJVDD000000000.1 DBLINK BioProject: PRJEB46020 BioSample: SAMEA8654747 KEYWORDS WGS. SOURCE Thunnus maccoyii (southern bluefin tuna) ORGANISM Thunnus maccoyii Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Pelagiaria; Scombriformes; Scombridae; Thunnus. REFERENCE 1 (bases 1 to 895) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (01-JUL-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Thunnus maccoyii whole genome shotgun (WGS) project has the project accession CAJVDD000000000. This version of the project (01) has the accession number CAJVDD010000000, and consists of sequences CAJVDD010000001-CAJVDD010000895. The assembly fThuMac1.1 is based on 46x PacBio data, 46x 10X Genomics Chromium data, BioNano data and Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 1 contains a large inversion between sister chromatids at approximately 2.7-9.5Mb. FEATURES Location/Qualifiers source 1..895 /organism="Thunnus maccoyii" /mol_type="genomic DNA" /db_xref="taxon:8240" WGS CAJVDD010000001-CAJVDD010000895 // LOCUS CAJZLI010000000 1192 rc DNA linear INV 18-SEP-2021 DEFINITION Platycheirus albimanus, whole genome shotgun sequencing project. ACCESSION CAJZLI000000000 VERSION CAJZLI000000000.1 DBLINK BioProject: PRJEB47513 BioSample: SAMEA7520157 Sequence Read Archive: ERR6054919, ERR6054920, ERR6054921, ERR6054922, ERR6054923, ERR6606791, ERR6606792 KEYWORDS WGS. SOURCE Platycheirus albimanus ORGANISM Platycheirus albimanus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Melanostomini; Platycheirus. REFERENCE 1 (bases 1 to 1192) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Platycheirus albimanus whole genome shotgun (WGS) project has the project accession CAJZLI000000000. This version of the project (01) has the accession number CAJZLI010000000, and consists of sequences CAJZLI010000001-CAJZLI010001192. The assembly idPlaAlba1.1 is based on 50x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The very large repetitive region of chromosome 1, spanning 119.95mb-193.61mb is less certain than the rest of the assembly. It has been assembled to best fit the Hi-C data. FEATURES Location/Qualifiers source 1..1192 /organism="Platycheirus albimanus" /mol_type="genomic DNA" /db_xref="taxon:414846" WGS CAJZLI010000001-CAJZLI010001192 // LOCUS CAJZLQ010000000 1200 rc DNA linear INV 18-SEP-2021 DEFINITION Bellardia pandia, whole genome shotgun sequencing project. ACCESSION CAJZLQ000000000 VERSION CAJZLQ000000000.1 DBLINK BioProject: PRJEB47512 BioSample: SAMEA7746779 KEYWORDS WGS. SOURCE Bellardia pandia ORGANISM Bellardia pandia Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Calliphoridae; Calliphorinae; Bellardia. REFERENCE 1 (bases 1 to 1200) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bellardia pandia whole genome shotgun (WGS) project has the project accession CAJZLQ000000000. This version of the project (01) has the accession number CAJZLQ010000000, and consists of sequences CAJZLQ010000001-CAJZLQ010001200. The assembly idBelPand1.1 is based on 54x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Several repetitive scaffolds remain unassigned to chromosomes. These are likely to belong to the X chromosome but a definitive placement cannot be made with current methods. FEATURES Location/Qualifiers source 1..1200 /organism="Bellardia pandia" /mol_type="genomic DNA" /db_xref="taxon:2795671" WGS CAJZLQ010000001-CAJZLQ010001200 // LOCUS CAJZLB010000000 2355 rc DNA linear PLN 18-SEP-2021 DEFINITION Malus sylvestris, whole genome shotgun sequencing project. ACCESSION CAJZLB000000000 VERSION CAJZLB000000000.1 DBLINK BioProject: PRJEB47503 BioSample: SAMEA9197672 KEYWORDS WGS. SOURCE Malus sylvestris ORGANISM Malus sylvestris Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 2355) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus sylvestris whole genome shotgun (WGS) project has the project accession CAJZLB000000000. This version of the project (01) has the accession number CAJZLB010000000, and consists of sequences CAJZLB010000001-CAJZLB010002355. The assembly drMalSylv7.1 is based on 15x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654 for Malus domestica. The Hi-C map provides evidence of inversions between haplotypes in chromosome 2 - 24.82-26.19Mb, and chromosome 11 - 17.06-19.05Mb. There are several scaffolds that it was possible to localize to a chromosome but not place, these have been labelled as unloc. Two of the largest unlocalised scaffolds -SUPER_4_unloc_1 and SUPER_14_unloc_1 - appear to be larger haplotypes of two specific loci; Chromosome 4 at 26.13-26.31Mb and Chromosome 14 at 782kb respectively. From the Hi-C it appears that these loci currently represent the shorter haplotype. As there is some uncertainty over these unloc scaffolds they have been left in the primary assembly. FEATURES Location/Qualifiers source 1..2355 /organism="Malus sylvestris" /mol_type="genomic DNA" /db_xref="taxon:3752" WGS CAJZLB010000001-CAJZLB010002355 // LOCUS CAJZHQ010000000 600 rc DNA linear PLN 18-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAJZHQ000000000 VERSION CAJZHQ000000000.1 DBLINK BioProject: PRJEB47506 BioSample: SAMEA9197673 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 600) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAJZHQ000000000. This version of the project (01) has the accession number CAJZHQ010000000, and consists of sequences CAJZHQ010000001-CAJZHQ010000600. The assembly drMalDome10.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654. Evidence of inversions between haplotypes from the Hi-C map in chromosome 4 21.72-23.32mb, chromosome 5 14.44-16.4mb and chromosome 11 30.76-33.27. FEATURES Location/Qualifiers source 1..600 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAJZHQ010000001-CAJZHQ010000600 // LOCUS CAJZHO010000000 949 rc DNA linear INV 18-SEP-2021 DEFINITION Spilarctia lutea, whole genome shotgun sequencing project. ACCESSION CAJZHO000000000 VERSION CAJZHO000000000.1 DBLINK BioProject: PRJEB47510 BioSample: SAMEA7631557 KEYWORDS WGS. SOURCE Spilarctia lutea ORGANISM Spilarctia lutea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Arctiinae; Spilarctia. REFERENCE 1 (bases 1 to 949) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Spilarctia lutea whole genome shotgun (WGS) project has the project accession CAJZHO000000000. This version of the project (01) has the accession number CAJZHO010000000, and consists of sequences CAJZHO010000001-CAJZHO010000949. The assembly ilSpiLutu1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..949 /organism="Spilarctia lutea" /mol_type="genomic DNA" /db_xref="taxon:875881" WGS CAJZHO010000001-CAJZHO010000949 // LOCUS CAJZHN010000000 1720 rc DNA linear INV 18-SEP-2021 DEFINITION Sacculina carcini, whole genome shotgun sequencing project. ACCESSION CAJZHN000000000 VERSION CAJZHN000000000.1 DBLINK BioProject: PRJEB47497 BioSample: SAMEA7522840 Sequence Read Archive: ERR6286729, ERR6286730, ERR6286731, ERR6286732, ERR6286733, ERR6412044 KEYWORDS WGS. SOURCE Sacculina carcini ORGANISM Sacculina carcini Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Multicrustacea; Hexanauplia; Cirripedia; Rhizocephala; Sacculinidae; Sacculina. REFERENCE 1 (bases 1 to 1720) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sacculina carcini whole genome shotgun (WGS) project has the project accession CAJZHN000000000. This version of the project (01) has the accession number CAJZHN010000000, and consists of sequences CAJZHN010000001-CAJZHN010001720. The assembly qxSacCarc1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1720 /organism="Sacculina carcini" /mol_type="genomic DNA" /db_xref="taxon:51650" WGS CAJZHN010000001-CAJZHN010001720 // LOCUS CAJZKA010000000 227 rc DNA linear INV 18-SEP-2021 DEFINITION Ancistrocerus nigricornis, whole genome shotgun sequencing project. ACCESSION CAJZKA000000000 VERSION CAJZKA000000000.1 DBLINK BioProject: PRJEB47508 BioSample: SAMEA7746762 KEYWORDS WGS. SOURCE Ancistrocerus nigricornis ORGANISM Ancistrocerus nigricornis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Eumeninae; Ancistrocerus. REFERENCE 1 (bases 1 to 227) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ancistrocerus nigricornis whole genome shotgun (WGS) project has the project accession CAJZKA000000000. This version of the project (01) has the accession number CAJZKA010000000, and consists of sequences CAJZKA010000001-CAJZKA010000227. The assembly iyAncNigr1.1 is based on 69x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. We are uncertain of the order and orientation of scaffolds on chromosome 1 between 15.0-21.1mb, although Hi-C shows that they localise to this repetitive centromeric/per-centromeric region. FEATURES Location/Qualifiers source 1..227 /organism="Ancistrocerus nigricornis" /mol_type="genomic DNA" /db_xref="taxon:76990" WGS CAJZKA010000001-CAJZKA010000227 // LOCUS CAJZHU010000000 68 rc DNA linear INV 18-SEP-2021 DEFINITION Bellardia pandia, whole genome shotgun sequencing project. ACCESSION CAJZHU000000000 VERSION CAJZHU000000000.1 DBLINK BioProject: PRJEB47511 BioSample: SAMEA7746779 KEYWORDS WGS. SOURCE Bellardia pandia ORGANISM Bellardia pandia Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Calliphoridae; Calliphorinae; Bellardia. REFERENCE 1 (bases 1 to 68) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bellardia pandia whole genome shotgun (WGS) project has the project accession CAJZHU000000000. This version of the project (01) has the accession number CAJZHU010000000, and consists of sequences CAJZHU010000001-CAJZHU010000068. The assembly idBelPand1.1 is based on 54x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Several repetitive scaffolds remain unassigned to chromosomes. These are likely to belong to the X chromosome but a definitive placement cannot be made with current methods. FEATURES Location/Qualifiers source 1..68 /organism="Bellardia pandia" /mol_type="genomic DNA" /db_xref="taxon:2795671" WGS CAJZHU010000001-CAJZHU010000068 // LOCUS CAJZLN010000000 9 rc DNA linear PLN 18-SEP-2021 DEFINITION Malus domestica, whole genome shotgun sequencing project. ACCESSION CAJZLN000000000 VERSION CAJZLN000000000.1 DBLINK BioProject: PRJEB47505 BioSample: SAMEA9197673 KEYWORDS WGS. SOURCE Malus domestica (apple) ORGANISM Malus domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus domestica whole genome shotgun (WGS) project has the project accession CAJZLN000000000. This version of the project (01) has the accession number CAJZLN010000000, and consists of sequences CAJZLN010000001-CAJZLN010000009. The assembly drMalDome10.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654. Evidence of inversions between haplotypes from the Hi-C map in chromosome 4 21.72-23.32mb, chromosome 5 14.44-16.4mb and chromosome 11 30.76-33.27. FEATURES Location/Qualifiers source 1..9 /organism="Malus domestica" /mol_type="genomic DNA" /db_xref="taxon:3750" WGS CAJZLN010000001-CAJZLN010000009 // LOCUS CAJZLR010000000 91 rc DNA linear INV 18-SEP-2021 DEFINITION Platycheirus albimanus, whole genome shotgun sequencing project. ACCESSION CAJZLR000000000 VERSION CAJZLR000000000.1 DBLINK BioProject: PRJEB47514 BioSample: SAMEA7520157 Sequence Read Archive: ERR6054919, ERR6054920, ERR6054921, ERR6054922, ERR6054923, ERR6606791, ERR6606792 KEYWORDS WGS. SOURCE Platycheirus albimanus ORGANISM Platycheirus albimanus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Melanostomini; Platycheirus. REFERENCE 1 (bases 1 to 91) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Platycheirus albimanus whole genome shotgun (WGS) project has the project accession CAJZLR000000000. This version of the project (01) has the accession number CAJZLR010000000, and consists of sequences CAJZLR010000001-CAJZLR010000091. The assembly idPlaAlba1.1 is based on 50x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The very large repetitive region of chromosome 1, spanning 119.95mb-193.61mb is less certain than the rest of the assembly. It has been assembled to best fit the Hi-C data. FEATURES Location/Qualifiers source 1..91 /organism="Platycheirus albimanus" /mol_type="genomic DNA" /db_xref="taxon:414846" WGS CAJZLR010000001-CAJZLR010000091 // LOCUS CAJZHC010000000 9 rc DNA linear INV 18-SEP-2021 DEFINITION Spilarctia lutea, whole genome shotgun sequencing project. ACCESSION CAJZHC000000000 VERSION CAJZHC000000000.1 DBLINK BioProject: PRJEB47509 BioSample: SAMEA7631557 KEYWORDS WGS. SOURCE Spilarctia lutea ORGANISM Spilarctia lutea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Arctiinae; Spilarctia. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Spilarctia lutea whole genome shotgun (WGS) project has the project accession CAJZHC000000000. This version of the project (01) has the accession number CAJZHC010000000, and consists of sequences CAJZHC010000001-CAJZHC010000009. The assembly ilSpiLutu1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..9 /organism="Spilarctia lutea" /mol_type="genomic DNA" /db_xref="taxon:875881" WGS CAJZHC010000001-CAJZHC010000009 // LOCUS CAJZIA010000000 17 rc DNA linear INV 18-SEP-2021 DEFINITION Sacculina carcini, whole genome shotgun sequencing project. ACCESSION CAJZIA000000000 VERSION CAJZIA000000000.1 DBLINK BioProject: PRJEB47498 BioSample: SAMEA7522840 Sequence Read Archive: ERR6286729, ERR6286730, ERR6286731, ERR6286732, ERR6286733, ERR6412044 KEYWORDS WGS. SOURCE Sacculina carcini ORGANISM Sacculina carcini Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Multicrustacea; Hexanauplia; Cirripedia; Rhizocephala; Sacculinidae; Sacculina. REFERENCE 1 (bases 1 to 17) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sacculina carcini whole genome shotgun (WGS) project has the project accession CAJZIA000000000. This version of the project (01) has the accession number CAJZIA010000000, and consists of sequences CAJZIA010000001-CAJZIA010000017. The assembly qxSacCarc1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..17 /organism="Sacculina carcini" /mol_type="genomic DNA" /db_xref="taxon:51650" WGS CAJZIA010000001-CAJZIA010000017 // LOCUS CAJZHM010000000 16 rc DNA linear PLN 18-SEP-2021 DEFINITION Malus sylvestris, whole genome shotgun sequencing project. ACCESSION CAJZHM000000000 VERSION CAJZHM000000000.1 DBLINK BioProject: PRJEB47504 BioSample: SAMEA9197672 KEYWORDS WGS. SOURCE Malus sylvestris ORGANISM Malus sylvestris Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Maleae; Malus. REFERENCE 1 (bases 1 to 16) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (13-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malus sylvestris whole genome shotgun (WGS) project has the project accession CAJZHM000000000. This version of the project (01) has the accession number CAJZHM010000000, and consists of sequences CAJZHM010000001-CAJZHM010000016. The assembly drMalSylv7.1 is based on 15x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of https://doi.org/10.1038/ng.654 for Malus domestica. The Hi-C map provides evidence of inversions between haplotypes in chromosome 2 - 24.82-26.19Mb, and chromosome 11 - 17.06-19.05Mb. There are several scaffolds that it was possible to localize to a chromosome but not place, these have been labelled as unloc. Two of the largest unlocalised scaffolds -SUPER_4_unloc_1 and SUPER_14_unloc_1 - appear to be larger haplotypes of two specific loci; Chromosome 4 at 26.13-26.31Mb and Chromosome 14 at 782kb respectively. From the Hi-C it appears that these loci currently represent the shorter haplotype. As there is some uncertainty over these unloc scaffolds they have been left in the primary assembly. FEATURES Location/Qualifiers source 1..16 /organism="Malus sylvestris" /mol_type="genomic DNA" /db_xref="taxon:3752" WGS CAJZHM010000001-CAJZHM010000016 // LOCUS CAJVDC010000000 33 rc DNA linear VRT 21-SEP-2021 DEFINITION Thunnus maccoyii, whole genome shotgun sequencing project. ACCESSION CAJVDC000000000 VERSION CAJVDC000000000.1 DBLINK BioProject: PRJEB46021 BioSample: SAMEA8654747 KEYWORDS WGS. SOURCE Thunnus maccoyii (southern bluefin tuna) ORGANISM Thunnus maccoyii Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Pelagiaria; Scombriformes; Scombridae; Thunnus. REFERENCE 1 (bases 1 to 33) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (01-JUL-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Thunnus maccoyii whole genome shotgun (WGS) project has the project accession CAJVDC000000000. This version of the project (01) has the accession number CAJVDC010000000, and consists of sequences CAJVDC010000001-CAJVDC010000033. The assembly fThuMac1.1 is based on 46x PacBio data, 46x 10X Genomics Chromium data, BioNano data and Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 1 contains a large inversion between sister chromatids at approximately 2.7-9.5Mb. FEATURES Location/Qualifiers source 1..33 /organism="Thunnus maccoyii" /mol_type="genomic DNA" /db_xref="taxon:8240" WGS CAJVDC010000001-CAJVDC010000033 // LOCUS CAJZBH010000000 5712 rc DNA linear INV 11-SEP-2021 DEFINITION Coremacera marginata, whole genome shotgun sequencing project. ACCESSION CAJZBH000000000 VERSION CAJZBH000000000.1 DBLINK BioProject: PRJEB47369 BioSample: SAMEA7521524 KEYWORDS WGS. SOURCE Coremacera marginata ORGANISM Coremacera marginata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Sciomyzoidea; Sciomyzidae; Coremacera. REFERENCE 1 (bases 1 to 5712) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Coremacera marginata whole genome shotgun (WGS) project has the project accession CAJZBH000000000. This version of the project (01) has the accession number CAJZBH010000000, and consists of sequences CAJZBH010000001-CAJZBH010005712. The assembly idCorMarg1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5712 /organism="Coremacera marginata" /mol_type="genomic DNA" /db_xref="taxon:1226616" WGS CAJZBH010000001-CAJZBH010005712 // LOCUS CAJZAY010000000 640 rc DNA linear VRT 11-SEP-2021 DEFINITION Thunnus albacares, whole genome shotgun sequencing project. ACCESSION CAJZAY000000000 VERSION CAJZAY000000000.1 DBLINK BioProject: PRJEB47266 BioSample: SAMEA8654749 KEYWORDS WGS. SOURCE Thunnus albacares (yellowfin tuna) ORGANISM Thunnus albacares Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Pelagiaria; Scombriformes; Scombridae; Thunnus. REFERENCE 1 (bases 1 to 640) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (31-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thunnus albacares whole genome shotgun (WGS) project has the project accession CAJZAY000000000. This version of the project (01) has the accession number CAJZAY010000000, and consists of sequences CAJZAY010000001-CAJZAY010000640. The assembly fThuAlb1.1 is based on 45x PacBio data, 42x 10X Genomics Chromium data, and Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..640 /organism="Thunnus albacares" /mol_type="genomic DNA" /db_xref="taxon:8236" WGS CAJZAY010000001-CAJZAY010000640 // LOCUS CAJZBV010000000 521 rc DNA linear INV 11-SEP-2021 DEFINITION Melanostoma mellinum, whole genome shotgun sequencing project. ACCESSION CAJZBV000000000 VERSION CAJZBV000000000.1 DBLINK BioProject: PRJEB47342 BioSample: SAMEA7520051 KEYWORDS WGS. SOURCE Melanostoma mellinum ORGANISM Melanostoma mellinum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Melanostomini; Melanostoma. REFERENCE 1 (bases 1 to 521) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Melanostoma mellinum whole genome shotgun (WGS) project has the project accession CAJZBV000000000. This version of the project (01) has the accession number CAJZBV010000000, and consists of sequences CAJZBV010000001-CAJZBV010000521. The assembly idMelMell2.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..521 /organism="Melanostoma mellinum" /mol_type="genomic DNA" /db_xref="taxon:653684" WGS CAJZBV010000001-CAJZBV010000521 // LOCUS CAJZBY010000000 910 rc DNA linear INV 11-SEP-2021 DEFINITION Thecocarcelia acutangulata, whole genome shotgun sequencing project. ACCESSION CAJZBY000000000 VERSION CAJZBY000000000.1 DBLINK BioProject: PRJEB47350 BioSample: SAMEA7746598 KEYWORDS WGS. SOURCE Thecocarcelia acutangulata ORGANISM Thecocarcelia acutangulata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Tachinidae; Exoristinae; Eryciini; Thecocarcelia. REFERENCE 1 (bases 1 to 910) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thecocarcelia acutangulata whole genome shotgun (WGS) project has the project accession CAJZBY000000000. This version of the project (01) has the accession number CAJZBY010000000, and consists of sequences CAJZBY010000001-CAJZBY010000910. The assembly idTheAcut1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..910 /organism="Thecocarcelia acutangulata" /mol_type="genomic DNA" /db_xref="taxon:1918310" WGS CAJZBY010000001-CAJZBY010000910 // LOCUS CAJZBP010000000 590 rc DNA linear INV 11-SEP-2021 DEFINITION Eilema depressum, whole genome shotgun sequencing project. ACCESSION CAJZBP000000000 VERSION CAJZBP000000000.1 DBLINK BioProject: PRJEB47359 BioSample: SAMEA7746611 KEYWORDS WGS. SOURCE Eilema depressum ORGANISM Eilema depressum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Arctiinae; Eilema. REFERENCE 1 (bases 1 to 590) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eilema depressum whole genome shotgun (WGS) project has the project accession CAJZBP000000000. This version of the project (01) has the accession number CAJZBP010000000, and consists of sequences CAJZBP010000001-CAJZBP010000590. The assembly ilEilDepe1.1 is based on 54x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..590 /organism="Eilema depressum" /mol_type="genomic DNA" /db_xref="taxon:987419" WGS CAJZBP010000001-CAJZBP010000590 // LOCUS CAJZBI010000000 139 rc DNA linear INV 11-SEP-2021 DEFINITION Agrochola circellaris, whole genome shotgun sequencing project. ACCESSION CAJZBI000000000 VERSION CAJZBI000000000.1 DBLINK BioProject: PRJEB47363 BioSample: SAMEA8603201 KEYWORDS WGS. SOURCE Agrochola circellaris ORGANISM Agrochola circellaris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Agrochola. REFERENCE 1 (bases 1 to 139) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Agrochola circellaris whole genome shotgun (WGS) project has the project accession CAJZBI000000000. This version of the project (01) has the accession number CAJZBI010000000, and consists of sequences CAJZBI010000001-CAJZBI010000139. The assembly ilAgrCirc1.1 is based on 33x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..139 /organism="Agrochola circellaris" /mol_type="genomic DNA" /db_xref="taxon:987866" WGS CAJZBI010000001-CAJZBI010000139 // LOCUS CAJZBE010000000 369 rc DNA linear INV 11-SEP-2021 DEFINITION Hydraecia micacea, whole genome shotgun sequencing project. ACCESSION CAJZBE000000000 VERSION CAJZBE000000000.1 DBLINK BioProject: PRJEB47368 BioSample: SAMEA8603188 KEYWORDS WGS. SOURCE Hydraecia micacea (rosy rustic) ORGANISM Hydraecia micacea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Apameini; Hydraecia. REFERENCE 1 (bases 1 to 369) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hydraecia micacea whole genome shotgun (WGS) project has the project accession CAJZBE000000000. This version of the project (01) has the accession number CAJZBE010000000, and consists of sequences CAJZBE010000001-CAJZBE010000369. The assembly ilHydMica1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..369 /organism="Hydraecia micacea" /mol_type="genomic DNA" /db_xref="taxon:214171" WGS CAJZBE010000001-CAJZBE010000369 // LOCUS CAJZBZ010000000 3981 rc DNA linear INV 11-SEP-2021 DEFINITION Sesia apiformis, whole genome shotgun sequencing project. ACCESSION CAJZBZ000000000 VERSION CAJZBZ000000000.1 DBLINK BioProject: PRJEB47346 BioSample: SAMEA7701281 KEYWORDS WGS. SOURCE Sesia apiformis ORGANISM Sesia apiformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sesioidea; Sesiidae; Sesiinae; Sesiini; Sesia. REFERENCE 1 (bases 1 to 3981) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sesia apiformis whole genome shotgun (WGS) project has the project accession CAJZBZ000000000. This version of the project (01) has the accession number CAJZBZ010000000, and consists of sequences CAJZBZ010000001-CAJZBZ010003981. The assembly ilSesApif2.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3981 /organism="Sesia apiformis" /mol_type="genomic DNA" /db_xref="taxon:748215" WGS CAJZBZ010000001-CAJZBZ010003981 // LOCUS CAJZBK010000000 550 rc DNA linear INV 11-SEP-2021 DEFINITION Agriopis aurantiaria, whole genome shotgun sequencing project. ACCESSION CAJZBK000000000 VERSION CAJZBK000000000.1 DBLINK BioProject: PRJEB47362 BioSample: SAMEA8603214 KEYWORDS WGS. SOURCE Agriopis aurantiaria ORGANISM Agriopis aurantiaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Agriopis. REFERENCE 1 (bases 1 to 550) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Agriopis aurantiaria whole genome shotgun (WGS) project has the project accession CAJZBK000000000. This version of the project (01) has the accession number CAJZBK010000000, and consists of sequences CAJZBK010000001-CAJZBK010000550. The assembly ilAgrAura1.1 is based on 35x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..550 /organism="Agriopis aurantiaria" /mol_type="genomic DNA" /db_xref="taxon:104476" WGS CAJZBK010000001-CAJZBK010000550 // LOCUS CAJZBO010000000 1215 rc DNA linear INV 11-SEP-2021 DEFINITION Anoplius nigerrimus, whole genome shotgun sequencing project. ACCESSION CAJZBO000000000 VERSION CAJZBO000000000.1 DBLINK BioProject: PRJEB47349 BioSample: SAMEA7746764 KEYWORDS WGS. SOURCE Anoplius nigerrimus ORGANISM Anoplius nigerrimus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Pompiloidea; Pompilidae; Pompilinae; Anoplius. REFERENCE 1 (bases 1 to 1215) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Anoplius nigerrimus whole genome shotgun (WGS) project has the project accession CAJZBO000000000. This version of the project (01) has the accession number CAJZBO010000000, and consists of sequences CAJZBO010000001-CAJZBO010001215. The assembly iyAnoNige1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1215 /organism="Anoplius nigerrimus" /mol_type="genomic DNA" /db_xref="taxon:1667466" WGS CAJZBO010000001-CAJZBO010001215 // LOCUS CAJZBJ010000000 165 rc DNA linear INV 11-SEP-2021 DEFINITION Eupsilia transversa, whole genome shotgun sequencing project. ACCESSION CAJZBJ000000000 VERSION CAJZBJ000000000.1 DBLINK BioProject: PRJEB47365 BioSample: SAMEA8563699 KEYWORDS WGS. SOURCE Eupsilia transversa (satellite moth) ORGANISM Eupsilia transversa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Ipimorphinae; Eupsilia. REFERENCE 1 (bases 1 to 165) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eupsilia transversa whole genome shotgun (WGS) project has the project accession CAJZBJ000000000. This version of the project (01) has the accession number CAJZBJ010000000, and consists of sequences CAJZBJ010000001-CAJZBJ010000165. The assembly ilEupTran1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..165 /organism="Eupsilia transversa" /mol_type="genomic DNA" /db_xref="taxon:116130" WGS CAJZBJ010000001-CAJZBJ010000165 // LOCUS CAJZBD010000000 418 rc DNA linear INV 11-SEP-2021 DEFINITION Harmonia axyridis, whole genome shotgun sequencing project. ACCESSION CAJZBD000000000 VERSION CAJZBD000000000.1 DBLINK BioProject: PRJEB47374 BioSample: SAMEA7520208 KEYWORDS WGS. SOURCE Harmonia axyridis ORGANISM Harmonia axyridis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Harmonia. REFERENCE 1 (bases 1 to 418) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Harmonia axyridis whole genome shotgun (WGS) project has the project accession CAJZBD000000000. This version of the project (01) has the accession number CAJZBD010000000, and consists of sequences CAJZBD010000001-CAJZBD010000418. The assembly icHarAxyr1.1 is based on 53x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. 7 curated autosomes and 1 allosome (X) curated for Harmonia axyridis. Some scaffolds remain unplaced due to repetitive content giving ambiguous HiC signal. Large cluster of rDNA sequences placed on X using HiC data only. FEATURES Location/Qualifiers source 1..418 /organism="Harmonia axyridis" /mol_type="genomic DNA" /db_xref="taxon:115357" WGS CAJZBD010000001-CAJZBD010000418 // LOCUS CAJZBM010000000 177 rc DNA linear INV 11-SEP-2021 DEFINITION Ptilodon capucinus, whole genome shotgun sequencing project. ACCESSION CAJZBM000000000 VERSION CAJZBM000000000.1 DBLINK BioProject: PRJEB47356 BioSample: SAMEA7746620 KEYWORDS WGS. SOURCE Ptilodon capucinus ORGANISM Ptilodon capucinus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Ptilodontinae; Ptilodon. REFERENCE 1 (bases 1 to 177) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ptilodon capucinus whole genome shotgun (WGS) project has the project accession CAJZBM000000000. This version of the project (01) has the accession number CAJZBM010000000, and consists of sequences CAJZBM010000001-CAJZBM010000177. The assembly ilPtiCapc1.1 is based on 55x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..177 /organism="Ptilodon capucinus" /mol_type="genomic DNA" /db_xref="taxon:987449" WGS CAJZBM010000001-CAJZBM010000177 // LOCUS CAJZBF010000000 278 rc DNA linear INV 11-SEP-2021 DEFINITION Membranipora membranacea, whole genome shotgun sequencing project. ACCESSION CAJZBF000000000 VERSION CAJZBF000000000.1 DBLINK BioProject: PRJEB47371 BioSample: SAMEA7536681 KEYWORDS WGS. SOURCE Membranipora membranacea ORGANISM Membranipora membranacea Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Bryozoa; Gymnolaemata; Cheilostomatida; Malacostegina; Membraniporoidea; Membraniporidae; Membranipora. REFERENCE 1 (bases 1 to 278) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Membranipora membranacea whole genome shotgun (WGS) project has the project accession CAJZBF000000000. This version of the project (01) has the accession number CAJZBF010000000, and consists of sequences CAJZBF010000001-CAJZBF010000278. The assembly tzMemMemb1.1 is based on 66x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..278 /organism="Membranipora membranacea" /mol_type="genomic DNA" /db_xref="taxon:95170" WGS CAJZBF010000001-CAJZBF010000278 // LOCUS CAJZBT010000000 407 rc DNA linear INV 11-SEP-2021 DEFINITION Tenthredo notha, whole genome shotgun sequencing project. ACCESSION CAJZBT000000000 VERSION CAJZBT000000000.1 DBLINK BioProject: PRJEB47354 BioSample: SAMEA7746761 KEYWORDS WGS. SOURCE Tenthredo notha ORGANISM Tenthredo notha Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Tenthredinoidea; Tenthredinidae; Tenthredininae; Tenthredo. REFERENCE 1 (bases 1 to 407) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Tenthredo notha whole genome shotgun (WGS) project has the project accession CAJZBT000000000. This version of the project (01) has the accession number CAJZBT010000000, and consists of sequences CAJZBT010000001-CAJZBT010000407. The assembly iyTenNoth1.1 is based on 77x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..407 /organism="Tenthredo notha" /mol_type="genomic DNA" /db_xref="taxon:362091" WGS CAJZBT010000001-CAJZBT010000407 // LOCUS CAJZBX010000000 1187 rc DNA linear INV 11-SEP-2021 DEFINITION Anoplius nigerrimus, whole genome shotgun sequencing project. ACCESSION CAJZBX000000000 VERSION CAJZBX000000000.1 DBLINK BioProject: PRJEB47348 BioSample: SAMEA7746764 KEYWORDS WGS. SOURCE Anoplius nigerrimus ORGANISM Anoplius nigerrimus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Pompiloidea; Pompilidae; Pompilinae; Anoplius. REFERENCE 1 (bases 1 to 1187) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Anoplius nigerrimus whole genome shotgun (WGS) project has the project accession CAJZBX000000000. This version of the project (01) has the accession number CAJZBX010000000, and consists of sequences CAJZBX010000001-CAJZBX010001187. The assembly iyAnoNige1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1187 /organism="Anoplius nigerrimus" /mol_type="genomic DNA" /db_xref="taxon:1667466" WGS CAJZBX010000001-CAJZBX010001187 // LOCUS CAJZBA010000000 266 rc DNA linear PLN 11-SEP-2021 DEFINITION Dunaliella primolecta, whole genome shotgun sequencing project. ACCESSION CAJZBA000000000 VERSION CAJZBA000000000.1 DBLINK BioProject: PRJEB47343 BioSample: SAMEA8100039 KEYWORDS WGS. SOURCE Dunaliella primolecta ORGANISM Dunaliella primolecta Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Chlorophyceae; CS clade; Chlamydomonadales; Dunaliellaceae; Dunaliella. REFERENCE 1 (bases 1 to 266) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dunaliella primolecta whole genome shotgun (WGS) project has the project accession CAJZBA000000000. This version of the project (01) has the accession number CAJZBA010000000, and consists of sequences CAJZBA010000001-CAJZBA010000266. The assembly ucDunPrim2.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..266 /organism="Dunaliella primolecta" /mol_type="genomic DNA" /db_xref="taxon:257627" WGS CAJZBA010000001-CAJZBA010000266 // LOCUS CAJZBB010000000 9 rc DNA linear PLN 11-SEP-2021 DEFINITION Dunaliella primolecta, whole genome shotgun sequencing project. ACCESSION CAJZBB000000000 VERSION CAJZBB000000000.1 DBLINK BioProject: PRJEB47344 BioSample: SAMEA8100039 KEYWORDS WGS. SOURCE Dunaliella primolecta ORGANISM Dunaliella primolecta Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Chlorophyceae; CS clade; Chlamydomonadales; Dunaliellaceae; Dunaliella. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dunaliella primolecta whole genome shotgun (WGS) project has the project accession CAJZBB000000000. This version of the project (01) has the accession number CAJZBB010000000, and consists of sequences CAJZBB010000001-CAJZBB010000009. The assembly ucDunPrim2.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..9 /organism="Dunaliella primolecta" /mol_type="genomic DNA" /db_xref="taxon:257627" WGS CAJZBB010000001-CAJZBB010000009 // LOCUS CAJZBU010000000 71 rc DNA linear INV 11-SEP-2021 DEFINITION Melanostoma mellinum, whole genome shotgun sequencing project. ACCESSION CAJZBU000000000 VERSION CAJZBU000000000.1 DBLINK BioProject: PRJEB47341 BioSample: SAMEA7520051 KEYWORDS WGS. SOURCE Melanostoma mellinum ORGANISM Melanostoma mellinum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Melanostomini; Melanostoma. REFERENCE 1 (bases 1 to 71) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Melanostoma mellinum whole genome shotgun (WGS) project has the project accession CAJZBU000000000. This version of the project (01) has the accession number CAJZBU010000000, and consists of sequences CAJZBU010000001-CAJZBU010000071. The assembly idMelMell2.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..71 /organism="Melanostoma mellinum" /mol_type="genomic DNA" /db_xref="taxon:653684" WGS CAJZBU010000001-CAJZBU010000071 // LOCUS CAJZCA010000000 47 rc DNA linear INV 11-SEP-2021 DEFINITION Thecocarcelia acutangulata, whole genome shotgun sequencing project. ACCESSION CAJZCA000000000 VERSION CAJZCA000000000.1 DBLINK BioProject: PRJEB47351 BioSample: SAMEA7746598 KEYWORDS WGS. SOURCE Thecocarcelia acutangulata ORGANISM Thecocarcelia acutangulata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Oestroidea; Tachinidae; Exoristinae; Eryciini; Thecocarcelia. REFERENCE 1 (bases 1 to 47) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thecocarcelia acutangulata whole genome shotgun (WGS) project has the project accession CAJZCA000000000. This version of the project (01) has the accession number CAJZCA010000000, and consists of sequences CAJZCA010000001-CAJZCA010000047. The assembly idTheAcut1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..47 /organism="Thecocarcelia acutangulata" /mol_type="genomic DNA" /db_xref="taxon:1918310" WGS CAJZCA010000001-CAJZCA010000047 // LOCUS CAJZBS010000000 54 rc DNA linear INV 11-SEP-2021 DEFINITION Coremacera marginata, whole genome shotgun sequencing project. ACCESSION CAJZBS000000000 VERSION CAJZBS000000000.1 DBLINK BioProject: PRJEB47370 BioSample: SAMEA7521524 KEYWORDS WGS. SOURCE Coremacera marginata ORGANISM Coremacera marginata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Sciomyzoidea; Sciomyzidae; Coremacera. REFERENCE 1 (bases 1 to 54) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Coremacera marginata whole genome shotgun (WGS) project has the project accession CAJZBS000000000. This version of the project (01) has the accession number CAJZBS010000000, and consists of sequences CAJZBS010000001-CAJZBS010000054. The assembly idCorMarg1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..54 /organism="Coremacera marginata" /mol_type="genomic DNA" /db_xref="taxon:1226616" WGS CAJZBS010000001-CAJZBS010000054 // LOCUS CAJZAX010000000 44 rc DNA linear VRT 11-SEP-2021 DEFINITION Thunnus albacares, whole genome shotgun sequencing project. ACCESSION CAJZAX000000000 VERSION CAJZAX000000000.1 DBLINK BioProject: PRJEB47267 BioSample: SAMEA8654749 KEYWORDS WGS. SOURCE Thunnus albacares (yellowfin tuna) ORGANISM Thunnus albacares Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Pelagiaria; Scombriformes; Scombridae; Thunnus. REFERENCE 1 (bases 1 to 44) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (31-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thunnus albacares whole genome shotgun (WGS) project has the project accession CAJZAX000000000. This version of the project (01) has the accession number CAJZAX010000000, and consists of sequences CAJZAX010000001-CAJZAX010000044. The assembly fThuAlb1.1 is based on 45x PacBio data, 42x 10X Genomics Chromium data, and Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..44 /organism="Thunnus albacares" /mol_type="genomic DNA" /db_xref="taxon:8236" WGS CAJZAX010000001-CAJZAX010000044 // LOCUS CAJZBN010000000 5 rc DNA linear INV 11-SEP-2021 DEFINITION Harmonia axyridis, whole genome shotgun sequencing project. ACCESSION CAJZBN000000000 VERSION CAJZBN000000000.1 DBLINK BioProject: PRJEB47373 BioSample: SAMEA7520208 KEYWORDS WGS. SOURCE Harmonia axyridis ORGANISM Harmonia axyridis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Harmonia. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Harmonia axyridis whole genome shotgun (WGS) project has the project accession CAJZBN000000000. This version of the project (01) has the accession number CAJZBN010000000, and consists of sequences CAJZBN010000001-CAJZBN010000005. The assembly icHarAxyr1.1 is based on 53x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. 7 curated autosomes and 1 allosome (X) curated for Harmonia axyridis. Some scaffolds remain unplaced due to repetitive content giving ambiguous HiC signal. Large cluster of rDNA sequences placed on X using HiC data only. FEATURES Location/Qualifiers source 1..5 /organism="Harmonia axyridis" /mol_type="genomic DNA" /db_xref="taxon:115357" WGS CAJZBN010000001-CAJZBN010000005 // LOCUS CAJZBL010000000 7 rc DNA linear INV 11-SEP-2021 DEFINITION Tenthredo notha, whole genome shotgun sequencing project. ACCESSION CAJZBL000000000 VERSION CAJZBL000000000.1 DBLINK BioProject: PRJEB47355 BioSample: SAMEA7746761 KEYWORDS WGS. SOURCE Tenthredo notha ORGANISM Tenthredo notha Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Tenthredinoidea; Tenthredinidae; Tenthredininae; Tenthredo. REFERENCE 1 (bases 1 to 7) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Tenthredo notha whole genome shotgun (WGS) project has the project accession CAJZBL000000000. This version of the project (01) has the accession number CAJZBL010000000, and consists of sequences CAJZBL010000001-CAJZBL010000007. The assembly iyTenNoth1.1 is based on 77x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..7 /organism="Tenthredo notha" /mol_type="genomic DNA" /db_xref="taxon:362091" WGS CAJZBL010000001-CAJZBL010000007 // LOCUS CAJZBG010000000 4 rc DNA linear INV 11-SEP-2021 DEFINITION Agrochola circellaris, whole genome shotgun sequencing project. ACCESSION CAJZBG000000000 VERSION CAJZBG000000000.1 DBLINK BioProject: PRJEB47364 BioSample: SAMEA8603201 KEYWORDS WGS. SOURCE Agrochola circellaris ORGANISM Agrochola circellaris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Xyleninae; Agrochola. REFERENCE 1 (bases 1 to 4) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Agrochola circellaris whole genome shotgun (WGS) project has the project accession CAJZBG000000000. This version of the project (01) has the accession number CAJZBG010000000, and consists of sequences CAJZBG010000001-CAJZBG010000004. The assembly ilAgrCirc1.1 is based on 33x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4 /organism="Agrochola circellaris" /mol_type="genomic DNA" /db_xref="taxon:987866" WGS CAJZBG010000001-CAJZBG010000004 // LOCUS CAJZBW010000000 10 rc DNA linear INV 11-SEP-2021 DEFINITION Membranipora membranacea, whole genome shotgun sequencing project. ACCESSION CAJZBW000000000 VERSION CAJZBW000000000.1 DBLINK BioProject: PRJEB47372 BioSample: SAMEA7536681 KEYWORDS WGS. SOURCE Membranipora membranacea ORGANISM Membranipora membranacea Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Bryozoa; Gymnolaemata; Cheilostomatida; Malacostegina; Membraniporoidea; Membraniporidae; Membranipora. REFERENCE 1 (bases 1 to 10) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Membranipora membranacea whole genome shotgun (WGS) project has the project accession CAJZBW000000000. This version of the project (01) has the accession number CAJZBW010000000, and consists of sequences CAJZBW010000001-CAJZBW010000010. The assembly tzMemMemb1.1 is based on 66x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..10 /organism="Membranipora membranacea" /mol_type="genomic DNA" /db_xref="taxon:95170" WGS CAJZBW010000001-CAJZBW010000010 // LOCUS CAJZBR010000000 4 rc DNA linear INV 11-SEP-2021 DEFINITION Sesia apiformis, whole genome shotgun sequencing project. ACCESSION CAJZBR000000000 VERSION CAJZBR000000000.1 DBLINK BioProject: PRJEB47347 BioSample: SAMEA7701281 KEYWORDS WGS. SOURCE Sesia apiformis ORGANISM Sesia apiformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sesioidea; Sesiidae; Sesiinae; Sesiini; Sesia. REFERENCE 1 (bases 1 to 4) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Sesia apiformis whole genome shotgun (WGS) project has the project accession CAJZBR000000000. This version of the project (01) has the accession number CAJZBR010000000, and consists of sequences CAJZBR010000001-CAJZBR010000004. The assembly ilSesApif2.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4 /organism="Sesia apiformis" /mol_type="genomic DNA" /db_xref="taxon:748215" WGS CAJZBR010000001-CAJZBR010000004 // LOCUS CAJZBC010000000 3 rc DNA linear INV 11-SEP-2021 DEFINITION Hydraecia micacea, whole genome shotgun sequencing project. ACCESSION CAJZBC000000000 VERSION CAJZBC000000000.1 DBLINK BioProject: PRJEB47367 BioSample: SAMEA8603188 KEYWORDS WGS. SOURCE Hydraecia micacea (rosy rustic) ORGANISM Hydraecia micacea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Apameini; Hydraecia. REFERENCE 1 (bases 1 to 3) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (03-SEP-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hydraecia micacea whole genome shotgun (WGS) project has the project accession CAJZBC000000000. This version of the project (01) has the accession number CAJZBC010000000, and consists of sequences CAJZBC010000001-CAJZBC010000003. The assembly ilHydMica1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3 /organism="Hydraecia micacea" /mol_type="genomic DNA" /db_xref="taxon:214171" WGS CAJZBC010000001-CAJZBC010000003 // LOCUS JAHSPX010000000 2350 rc DNA linear PLN 14-SEP-2021 DEFINITION Arctostaphylos glauca isolate GLNDR_RDG_Rd-6, whole genome shotgun sequencing project. ACCESSION JAHSPX000000000 VERSION JAHSPX000000000.1 DBLINK BioProject: PRJNA735272 BioSample: SAMN19489519 KEYWORDS WGS. SOURCE Arctostaphylos glauca ORGANISM Arctostaphylos glauca Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Ericaceae; Arbutoideae; Arctostaphylos. REFERENCE 1 (bases 1 to 2350) AUTHORS Escalona,M., Huang,Y., Morrison,G., Litt,A. and Toffelmeier,E. TITLE Reference genome assembly of the Big Berry Manzanita (Arctostaphylos glauca) JOURNAL Unpublished REFERENCE 2 (bases 1 to 2350) AUTHORS Escalona,M., Huang,Y., Morrison,G., Litt,A. and Toffelmeier,E. TITLE Direct Submission JOURNAL Submitted (24-JUN-2021) Ecology and Evolutionary Biology, UCLA, 610 Charles Young Drive South, Los Angeles, CA 90095, USA COMMENT The Arctostaphylos glauca whole genome shotgun (WGS) project has the project accession JAHSPX000000000. This version of the project (01) has the accession number JAHSPX010000000, and consists of sequences JAHSPX010000001-JAHSPX010002350. ##Genome-Assembly-Data-START## Assembly Date :: 04-JUN-2021 Assembly Method :: HiFiasm v. 0.13-r308; purge_dups v. 1.2.5; SALSA v. 2.1 Assembly Name :: ddArcGlau1.0.a Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 45x Sequencing Technology :: PacBio HiFi (Sequel II); Dovetail HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2350 /organism="Arctostaphylos glauca" /mol_type="genomic DNA" /isolate="GLNDR_RDG_Rd-6" /specimen_voucher="Morrison 13" /db_xref="taxon:89197" /tissue_type="Floral buds" /dev_stage="flowering" /country="USA: Glendora Ridge Rd, San Gabriel Mountain, California" /lat_lon="34.20649 N 117.78815 W" /collection_date="2018-02-19" /collected_by="Glen Morrison, Yi Huang, Amy Litt" WGS JAHSPX010000001-JAHSPX010002350 // LOCUS JAHSPW010000000 271 rc DNA linear PLN 14-SEP-2021 DEFINITION Arctostaphylos glauca isolate GLNDR_RDG_Rd-6, whole genome shotgun sequencing project. ACCESSION JAHSPW000000000 VERSION JAHSPW000000000.1 DBLINK BioProject: PRJNA735273 BioSample: SAMN19489519 KEYWORDS WGS. SOURCE Arctostaphylos glauca ORGANISM Arctostaphylos glauca Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Ericaceae; Arbutoideae; Arctostaphylos. REFERENCE 1 (bases 1 to 271) AUTHORS Escalona,M., Huang,Y., Morrison,G., Litt,A. and Toffelmeier,E. TITLE Reference genome assembly of the Big Berry Manzanita (Arctostaphylos glauca) JOURNAL Unpublished REFERENCE 2 (bases 1 to 271) AUTHORS Escalona,M., Huang,Y., Morrison,G., Litt,A. and Toffelmeier,E. TITLE Direct Submission JOURNAL Submitted (16-JUN-2021) Ecology and Evolutionary Biology, UCLA, 610 Charles Young Drive South, Los Angeles, CA 90095, USA COMMENT The Arctostaphylos glauca whole genome shotgun (WGS) project has the project accession JAHSPW000000000. This version of the project (01) has the accession number JAHSPW010000000, and consists of sequences JAHSPW010000001-JAHSPW010000271. ##Genome-Assembly-Data-START## Assembly Date :: 04-JUN-2021 Assembly Method :: HiFiasm v. 0.13-r308; purge_dups v. 1.2.5; SALSA v. 2.1 Assembly Name :: ddArcGlau1.0.p Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 45x Sequencing Technology :: PacBio HiFi (Sequel II); Dovetail HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..271 /organism="Arctostaphylos glauca" /mol_type="genomic DNA" /isolate="GLNDR_RDG_Rd-6" /specimen_voucher="Morrison 13" /db_xref="taxon:89197" /tissue_type="Floral buds" /dev_stage="flowering" /country="USA: Glendora Ridge Rd, San Gabriel Mountain, California" /lat_lon="34.20649 N 117.78815 W" /collection_date="2018-02-19" /collected_by="Glen Morrison, Yi Huang, Amy Litt" WGS JAHSPW010000001-JAHSPW010000271 // LOCUS WSPL04000000 41 rc DNA linear VRT 25-AUG-2021 DEFINITION Dermochelys coriacea isolate rDerCor1, whole genome shotgun sequencing project. ACCESSION WSPL00000000 VERSION WSPL00000000.4 DBLINK BioProject: PRJNA561993 BioSample: SAMN12629498 KEYWORDS WGS. SOURCE Dermochelys coriacea (leatherback sea turtle) ORGANISM Dermochelys coriacea Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Americhelydia; Chelonioidea; Dermochelyidae; Dermochelys. REFERENCE 1 (bases 1 to 41) AUTHORS Komoroske,L., Fedrigo,O., Mountcastle,J., Uliano Da Silva,M., Haase,B., Formenti,G., Chow,W., Howe,K., Gilbert,M.T.P., Flicek,P., Gemmell,N., Marques,T., Scott,A., Murphy,R., Bjorndal,K., Braun,E., Rhie,A., Tracey,A., Sims,Y., Thibaud-Nissen,F., Phillippy,A. and Jarvis,E.D. TITLE (UPDATE) Dermochelys coriacea (Leatherback Sea Turtle) genome, rDerCor1, primary haplotype, v4 JOURNAL Unpublished REFERENCE 2 (bases 1 to 41) AUTHORS Komoroske,L., Fedrigo,O., Mountcastle,J., Uliano Da Silva,M., Haase,B., Formenti,G., Chow,W., Howe,K., Gilbert,M.T.P., Flicek,P., Gemmell,N., Marques,T., Scott,A., Murphy,R., Bjorndal,K., Braun,E., Rhie,A., Phillippy,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (05-DEC-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 41) AUTHORS Komoroske,L., Fedrigo,O., Mountcastle,J., Uliano Da Silva,M., Haase,B., Formenti,G., Chow,W., Howe,K., Gilbert,M.T.P., Flicek,P., Gemmell,N., Marques,T., Scott,A., Murphy,R., Bjorndal,K., Braun,E., Rhie,A., Tracey,A., Sims,Y., Thibaud-Nissen,F., Phillippy,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (25-JUL-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Aug 16, 2021 this sequence version replaced WSPL00000000.3. The Dermochelys coriacea whole genome shotgun (WGS) project has the project accession WSPL00000000. This version of the project (04) has the accession number WSPL04000000, and consists of sequences WSPL04000001-WSPL04000041. ##Genome-Assembly-Data-START## Assembly Date :: 24-MAY-2021 Assembly Method :: FALCON DNANexus v. 1.9.0; FALCON-Unzip DNANexus v. 1.0.6; purge_dups v. v1; scaff10x v. 4.1.0; Bionano Solve DLS v. 3.2.1; Salsa HiC v. 2.2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 6.0.0.47841; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2021-05-24; VGP assembly pipeline individual v. 1.6 Assembly Name :: rDerCor1.pri.v4 Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 63.68x Sequencing Technology :: PacBio Sequel I CLR; llumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..41 /organism="Dermochelys coriacea" /mol_type="genomic DNA" /isolate="rDerCor1" /db_xref="taxon:27794" /sex="male" /tissue_type="blood" /dev_stage="adult" /country="USA: Half Moon Bay, California" /lat_lon="37.46311 N 122.4293 W" /collection_date="2017-09-26" /collected_by="Lisa Komoroske" WGS WSPL04000001-WSPL04000041 WGS_SCAFLD CM019935-CM019962 WGS_SCAFLD CM019965 // LOCUS CAJVWD010000000 199 rc DNA linear INV 18-AUG-2021 DEFINITION Hydriomena furcata, whole genome shotgun sequencing project. ACCESSION CAJVWD000000000 VERSION CAJVWD000000000.1 DBLINK BioProject: PRJEB47025 BioSample: SAMEA7701301 KEYWORDS WGS. SOURCE Hydriomena furcata ORGANISM Hydriomena furcata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Larentiinae; Hydriomena. REFERENCE 1 (bases 1 to 199) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hydriomena furcata whole genome shotgun (WGS) project has the project accession CAJVWD000000000. This version of the project (01) has the accession number CAJVWD010000000, and consists of sequences CAJVWD010000001-CAJVWD010000199. The assembly ilHydFurc1.1 is based on 42x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..199 /organism="Hydriomena furcata" /mol_type="genomic DNA" /db_xref="taxon:104460" WGS CAJVWD010000001-CAJVWD010000199 // LOCUS CAJVWE010000000 341 rc DNA linear INV 18-AUG-2021 DEFINITION Campaea margaritaria, whole genome shotgun sequencing project. ACCESSION CAJVWE000000000 VERSION CAJVWE000000000.1 DBLINK BioProject: PRJEB47022 BioSample: SAMEA7701535 KEYWORDS WGS. SOURCE Campaea margaritaria ORGANISM Campaea margaritaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Campaea. REFERENCE 1 (bases 1 to 341) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Campaea margaritaria whole genome shotgun (WGS) project has the project accession CAJVWE000000000. This version of the project (01) has the accession number CAJVWE010000000, and consists of sequences CAJVWE010000001-CAJVWE010000341. The assembly ilCamMarg1.1 is based on 48x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..341 /organism="Campaea margaritaria" /mol_type="genomic DNA" /db_xref="taxon:934813" WGS CAJVWE010000001-CAJVWE010000341 // LOCUS CAJVWB010000000 36 rc DNA linear INV 18-AUG-2021 DEFINITION Papilio machaon, whole genome shotgun sequencing project. ACCESSION CAJVWB000000000 VERSION CAJVWB000000000.1 DBLINK BioProject: PRJEB47026 BioSample: SAMEA7523121 KEYWORDS WGS. SOURCE Papilio machaon (common yellow swallowtail) ORGANISM Papilio machaon Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Papilionidae; Papilioninae; Papilio. REFERENCE 1 (bases 1 to 36) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Papilio machaon whole genome shotgun (WGS) project has the project accession CAJVWB000000000. This version of the project (01) has the accession number CAJVWB010000000, and consists of sequences CAJVWB010000001-CAJVWB010000036. The assembly ilPapMach1.1 is based on 99x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..36 /organism="Papilio machaon" /mol_type="genomic DNA" /db_xref="taxon:76193" WGS CAJVWB010000001-CAJVWB010000036 // LOCUS CAJVWA010000000 130 rc DNA linear INV 18-AUG-2021 DEFINITION Aporia crataegi, whole genome shotgun sequencing project. ACCESSION CAJVWA000000000 VERSION CAJVWA000000000.1 DBLINK BioProject: PRJEB47021 BioSample: SAMEA7523355 KEYWORDS WGS. SOURCE Aporia crataegi ORGANISM Aporia crataegi Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Pierinae; Aporia. REFERENCE 1 (bases 1 to 130) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Aporia crataegi whole genome shotgun (WGS) project has the project accession CAJVWA000000000. This version of the project (01) has the accession number CAJVWA010000000, and consists of sequences CAJVWA010000001-CAJVWA010000130. The assembly ilApoCrat1.1 is based on 101x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..130 /organism="Aporia crataegi" /mol_type="genomic DNA" /db_xref="taxon:129397" WGS CAJVWA010000001-CAJVWA010000130 // LOCUS CAJVWF010000000 6 rc DNA linear INV 18-AUG-2021 DEFINITION Hydriomena furcata, whole genome shotgun sequencing project. ACCESSION CAJVWF000000000 VERSION CAJVWF000000000.1 DBLINK BioProject: PRJEB47024 BioSample: SAMEA7701301 KEYWORDS WGS. SOURCE Hydriomena furcata ORGANISM Hydriomena furcata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Larentiinae; Hydriomena. REFERENCE 1 (bases 1 to 6) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hydriomena furcata whole genome shotgun (WGS) project has the project accession CAJVWF000000000. This version of the project (01) has the accession number CAJVWF010000000, and consists of sequences CAJVWF010000001-CAJVWF010000006. The assembly ilHydFurc1.1 is based on 42x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..6 /organism="Hydriomena furcata" /mol_type="genomic DNA" /db_xref="taxon:104460" WGS CAJVWF010000001-CAJVWF010000006 // LOCUS CAJVWC010000000 2 rc DNA linear INV 18-AUG-2021 DEFINITION Papilio machaon, whole genome shotgun sequencing project. ACCESSION CAJVWC000000000 VERSION CAJVWC000000000.1 DBLINK BioProject: PRJEB47027 BioSample: SAMEA7523121 KEYWORDS WGS. SOURCE Papilio machaon (common yellow swallowtail) ORGANISM Papilio machaon Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Papilionidae; Papilioninae; Papilio. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (16-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Papilio machaon whole genome shotgun (WGS) project has the project accession CAJVWC000000000. This version of the project (01) has the accession number CAJVWC010000000, and consists of sequences CAJVWC010000001-CAJVWC010000002. The assembly ilPapMach1.1 is based on 99x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Papilio machaon" /mol_type="genomic DNA" /db_xref="taxon:76193" WGS CAJVWC010000001-CAJVWC010000002 // LOCUS CAJHXB020000000 2586 rc DNA linear INV 16-AUG-2021 DEFINITION Phalera bucephala, whole genome shotgun sequencing project. ACCESSION CAJHXB000000000 VERSION CAJHXB000000000.2 DBLINK BioProject: PRJEB41947 BioSample: SAMEA7519921 KEYWORDS WGS. SOURCE Phalera bucephala ORGANISM Phalera bucephala Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Phalerinae; Phalera. REFERENCE 1 (bases 1 to 2586) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 2586) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-AUG-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Aug 16, 2021 this sequence version replaced CAJHXB000000000.1. The Phalera bucephala whole genome shotgun (WGS) project has the project accession CAJHXB000000000. This version of the project (02) has the accession number CAJHXB020000000, and consists of sequences CAJHXB020000001-CAJHXB020002586. The assembly ilPhaBuce1.2 is based on 34x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2586 /organism="Phalera bucephala" /mol_type="genomic DNA" /db_xref="taxon:753216" WGS CAJHXB020000001-CAJHXB020002586 // LOCUS CAJHXA020000000 85 rc DNA linear INV 16-AUG-2021 DEFINITION Phalera bucephala, whole genome shotgun sequencing project. ACCESSION CAJHXA000000000 VERSION CAJHXA000000000.2 DBLINK BioProject: PRJEB41948 BioSample: SAMEA7519921 KEYWORDS WGS. SOURCE Phalera bucephala ORGANISM Phalera bucephala Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Phalerinae; Phalera. REFERENCE 1 (bases 1 to 85) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-DEC-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 85) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-AUG-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Aug 16, 2021 this sequence version replaced CAJHXA000000000.1. The Phalera bucephala whole genome shotgun (WGS) project has the project accession CAJHXA000000000. This version of the project (02) has the accession number CAJHXA020000000, and consists of sequences CAJHXA020000001-CAJHXA020000085. The assembly ilPhaBuce1.2 is based on 34x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..85 /organism="Phalera bucephala" /mol_type="genomic DNA" /db_xref="taxon:753216" WGS CAJHXA020000001-CAJHXA020000085 // LOCUS CAJVVO010000000 739 rc DNA linear INV 14-AUG-2021 DEFINITION Vespa velutina, whole genome shotgun sequencing project. ACCESSION CAJVVO000000000 VERSION CAJVVO000000000.1 DBLINK BioProject: PRJEB46980 BioSample: SAMEA5248726 KEYWORDS WGS. SOURCE Vespa velutina ORGANISM Vespa velutina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespa. REFERENCE 1 (bases 1 to 739) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (12-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespa velutina whole genome shotgun (WGS) project has the project accession CAJVVO000000000. This version of the project (01) has the accession number CAJVVO010000000, and consists of sequences CAJVVO010000001-CAJVVO010000739. The assembly iVesVel2.1 is based on 56x PacBio data and 94x 10X Genomics Chromium data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: palindromic read correction with pbclip, initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, Hi-C based scaffolding with SALSA2, Arrow polishing, and short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger. The mitochondrial assembly was produced using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..739 /organism="Vespa velutina" /mol_type="genomic DNA" /db_xref="taxon:202808" WGS CAJVVO010000001-CAJVVO010000739 // LOCUS CAJVVP010000000 17 rc DNA linear INV 14-AUG-2021 DEFINITION Vespa velutina, whole genome shotgun sequencing project. ACCESSION CAJVVP000000000 VERSION CAJVVP000000000.1 DBLINK BioProject: PRJEB46979 BioSample: SAMEA5248726 KEYWORDS WGS. SOURCE Vespa velutina ORGANISM Vespa velutina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespa. REFERENCE 1 (bases 1 to 17) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (12-AUG-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespa velutina whole genome shotgun (WGS) project has the project accession CAJVVP000000000. This version of the project (01) has the accession number CAJVVP010000000, and consists of sequences CAJVVP010000001-CAJVVP010000017. The assembly iVesVel2.1 is based on 56x PacBio data and 94x 10X Genomics Chromium data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: palindromic read correction with pbclip, initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, Hi-C based scaffolding with SALSA2, Arrow polishing, and short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger. The mitochondrial assembly was produced using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..17 /organism="Vespa velutina" /mol_type="genomic DNA" /db_xref="taxon:202808" WGS CAJVVP010000001-CAJVVP010000017 // LOCUS RRCC02000000 1646 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Black17, whole genome shotgun sequencing project. ACCESSION RRCC00000000 VERSION RRCC00000000.2 DBLINK BioProject: PRJNA489099 BioSample: SAMN02981239 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 1646) AUTHORS Warren,W.C., Clayton,D.F., Ellegren,H., Arnold,A.P., Hillier,L.W., Kunstner,A., Searle,S., White,S., Vilella,A.J., Fairley,S., Heger,A., Kong,L., Ponting,C.P., Jarvis,E.D., Mello,C.V., Minx,P., Lovell,P., Velho,T.A., Ferris,M., Balakrishnan,C.N., Sinha,S., Blatti,C., London,S.E., Li,Y., Lin,Y.C., George,J., Sweedler,J., Southey,B., Gunaratne,P., Watson,M., Nam,K., Backstrom,N., Smeds,L., Nabholz,B., Itoh,Y., Whitney,O., Pfenning,A.R., Howard,J., Volker,M., Skinner,B.M., Griffin,D.K., Ye,L., McLaren,W.M., Flicek,P., Quesada,V., Velasco,G., Lopez-Otin,C., Puente,X.S., Olender,T., Lancet,D., Smit,A.F., Hubley,R., Konkel,M.K., Walker,J.A., Batzer,M.A., Gu,W., Pollock,D.D., Chen,L., Cheng,Z., Eichler,E.E., Stapley,J., Slate,J., Ekblom,R., Birkhead,T., Burke,T., Burt,D., Scharff,C., Adam,I., Richard,H., Sultan,M., Soldatov,A., Lehrach,H., Edwards,S.V., Yang,S.P., Li,X., Graves,T., Fulton,L., Nelson,J., Chinwalla,A., Hou,S., Mardis,E.R. and Wilson,R.K. TITLE The genome of a songbird JOURNAL Nature 464 (7289), 757-762 (2010) PUBMED 20360741 REFERENCE 2 (bases 1 to 1646) AUTHORS Korlach,J., Gedman,G., Kingan,S.B., Chin,C.S., Howard,J.T., Audet,J.N., Cantin,L. and Jarvis,E.D. TITLE De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads JOURNAL Gigascience 6 (10), 1-16 (2017) PUBMED 29020750 REFERENCE 3 (bases 1 to 1646) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 4 (bases 1 to 1646) AUTHORS Jarvis,E.D., Rhie,A., Korlach,J., Fedrigo,O., Mountcastle,J., Haase,B., Koren,S., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Burt,D., Warren,W., Selvaraj,S., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (06-NOV-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 1646) AUTHORS Jarvis,E.D., Rhie,A., Korlach,J., Formenti,G., Mountcastle,J., Koren,S., Howe,K., Chow,W., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Burt,D., Warren,W., Selvaraj,S., Mello,C.V., Brown,S. and Fedrigo,O. TITLE Direct Submission JOURNAL Submitted (23-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 28, 2021 this sequence version replaced RRCC00000000.1. The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession RRCC00000000. This version of the project (02) has the accession number RRCC02000000, and consists of sequences RRCC02000001-RRCC02001646. ##Genome-Assembly-Data-START## Assembly Date :: 09-APR-2021 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. Nov2017(uc4); Purge_dups v. 1.0.1; Scaff10X v. 3.2.1; Bionano Solve BspQI/BssSI v. 3.4; Salsa2 v. 2.2; Arrow polishing v. variantCaller 2.3.3; Merfin filtering v. 0.1; longranger align v. 2.2.2; freebayes polishing v. 1.3.1; gEVAL manual curation v. 2021-04-09; VGP pipeline v. 1.7 Assembly Name :: bTaeGut1.4.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 88.2x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1646 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Black17" /db_xref="taxon:59729" /sex="male" WGS RRCC02000001-RRCC02001646 // LOCUS RRCB02000000 198 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Black17, whole genome shotgun sequencing project. ACCESSION RRCB00000000 VERSION RRCB00000000.2 DBLINK BioProject: PRJNA489098 BioSample: SAMN02981239 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 198) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 198) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 198) AUTHORS Jarvis,E.D., Rhie,A., Korlach,J., Fedrigo,O., Mountcastle,J., Koren,S., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Burt,D., Warren,W., Selvaraj,S. and Mello,C.V. TITLE Direct Submission JOURNAL Submitted (06-NOV-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 4 (bases 1 to 198) AUTHORS Jarvis,E.D., Rhie,A., Korlach,J., Formenti,G., Mountcastle,J., Koren,S., Howe,K., Chow,W., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Burt,D., Warren,W., Selvaraj,S., Mello,C.V., Brown,S. and Fedrigo,O. TITLE Direct Submission JOURNAL Submitted (23-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 28, 2021 this sequence version replaced RRCB00000000.1. The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession RRCB00000000. This version of the project (02) has the accession number RRCB02000000, and consists of sequences RRCB02000001-RRCB02000198. This assembly, bTaeGut1.4.pri, is a revised version 4 assembly of the male zebra finch bTaeGut1, using the VGP pipeline v1.7 to remove more false gene duplications, increase genome assembly continguity, and identify additional chromosomes. It includes the W sex chromosome accession CM018260.2 from the assembly of female bTaeGut2 (GCA_008822105.2) to include the W and Z sex chromosomes in the same assembly. ##Genome-Assembly-Data-START## Assembly Date :: 09-APR-2021 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. Nov2017(uc4); Purge_dups v. 1.0.1; Scaff10X v. 4.1.0; Bionano Solve BspQI/BssSI v. 3.4; Salsa2 v. 2.2.; Arrow polishing v. variantCaller 2.3.3; Merfin filtering v. 0.1; longranger align v. 2.2.2; freebayes polishing v. 1.3.1; gEVAL manual curation v. 2021-04-09; VGP pipeline v. 1.7 Assembly Name :: bTaeGut1.4.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 88.2x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads; Bionano Genomics two enzymes; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..198 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Black17" /db_xref="taxon:59729" /sex="male" WGS RRCB02000001-RRCB02000198 WGS_SCAFLD CM012081-CM012113 WGS_SCAFLD CM016613 WGS_SCAFLD CM025860-CM025865 WGS_SCAFLD CM030979 // LOCUS VHLE02000000 55 rc DNA linear MAM 11-AUG-2021 DEFINITION Lynx canadensis isolate LIC74, whole genome shotgun sequencing project. ACCESSION VHLE00000000 VERSION VHLE00000000.2 DBLINK BioProject: PRJNA489107 BioSample: SAMN09948483 KEYWORDS WGS. SOURCE Lynx canadensis (Canada lynx) ORGANISM Lynx canadensis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Felinae; Lynx. REFERENCE 1 (bases 1 to 55) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 55) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 55) AUTHORS Lama,T., Johnson,W., Organ,J.F., Vashon,J., Fedrigo,O., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Collins,J., Chow,W., Howe,K., Lewin,H., Durbin,R., Myers,G., O'Brien,S., Koepfli,K.-P., Ryder,O., Damas,J., Formenti,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (21-JUN-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 4 (bases 1 to 55) AUTHORS Lama,T., Johnson,W., Organ,J.F., Vashon,J., Fedrigo,O., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Collins,J., Chow,W., Howe,K., Lewin,H., Durbin,R., Myers,G., O'Brien,S., Koepfli,K.-P., Ryder,O., Damas,J., Formenti,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (08-JUN-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Jun 16, 2020 this sequence version replaced VHLE00000000.1. The Lynx canadensis whole genome shotgun (WGS) project has the project accession VHLE00000000. This version of the project (02) has the accession number VHLE02000000, and consists of sequences VHLE02000001-VHLE02000055. This assembly represents the principal haplotype of the diploid genome Lynx canadensis and includes the chromosomes. The alternate haplotype sequences are in WGS project VHLF00000000. ##Genome-Assembly-Data-START## Assembly Date :: 03-APR-2020 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; purge_haplotigs v. bitbucket 7.10.2018; scaff10x v. 2.1; Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2020-04-03; VGP standard assembly pipeline v. 1.5 Assembly Name :: mLynCan4.pri.v2 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 72.0x Sequencing Technology :: PacBio Sequel I; 10X genome; Bionano Genomics; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..55 /organism="Lynx canadensis" /mol_type="genomic DNA" /isolate="LIC74" /db_xref="taxon:61383" /sex="male" /tissue_type="muscle, distal limb" /country="USA: Aroostook County, Maine" /lat_lon="42.2466 N 71.6746 W" /collection_date="2017-12-05" /collected_by="Tanya Lama" WGS VHLE02000001-VHLE02000055 WGS_SCAFLD CM017329-CM017348 WGS_SCAFLD CM023961 // LOCUS RXPB02000000 10857 rc DNA linear MAM 11-AUG-2021 DEFINITION Phyllostomus discolor isolate MPI-MPIP mPhyDis1, whole genome shotgun sequencing project. ACCESSION RXPB00000000 VERSION RXPB00000000.2 DBLINK BioProject: PRJNA489142 BioSample: SAMN09948786 KEYWORDS WGS. SOURCE Phyllostomus discolor (pale spear-nosed bat) ORGANISM Phyllostomus discolor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Phyllostomidae; Phyllostominae; Phyllostomus. REFERENCE 1 (bases 1 to 10857) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 10857) AUTHORS Teeling,E.C., Vernes,S.C., Davalos,L.M., Ray,D.A., Gilbert,M.T.P. and Myers,E. CONSRTM Bat1K Consortium TITLE Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species JOURNAL Annu Rev Anim Biosci 6, 23-46 (2018) PUBMED 29166127 REFERENCE 3 (bases 1 to 10857) AUTHORS Jebb,D., Huang,Z., Pippel,M., Hughes,G.M., Lavrichenko,K., Devanna,P., Winkler,S., Jermiin,L.S., Skirmuntt,E.C., Katzourakis,A., Burkitt-Gray,L., Ray,D.A., Sullivan,K.A.M., Roscito,J.G., Kirilenko,B.M., Davalos,L.M., Corthals,A.P., Power,M.L., Jones,G., Ransome,R.D., Dechmann,D.K.N., Locatelli,A.G., Puechmaille,S.J., Fedrigo,O., Jarvis,E.D., Hiller,M., Vernes,S.C., Myers,E.W. and Teeling,E.C. TITLE Six reference-quality genomes reveal evolution of bat adaptations JOURNAL Nature 583 (7817), 578-584 (2020) PUBMED 32699395 REFERENCE 4 (bases 1 to 10857) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 5 (bases 1 to 10857) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 6 (bases 1 to 10857) AUTHORS Vernes,S., Fedrigo,O., Teeling,E., Myers,G., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (17-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 7 (bases 1 to 10857) AUTHORS Vernes,S., Fedrigo,O., Teeling,E., Myers,G., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Formenti,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (05-MAY-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On May 11, 2020 this sequence version replaced RXPB00000000.1. The Phyllostomus discolor whole genome shotgun (WGS) project has the project accession RXPB00000000. This version of the project (02) has the accession number RXPB02000000, and consists of sequences RXPB02000001-RXPB02010857. This assembly represents the alternate haplotype of the diploid genome Phyllostomus discolor. The principal haplotype sequences are in WGS project RXPA00000000. ##Genome-Assembly-Data-START## Assembly Date :: 29-NOV-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip 1.0.2 v. 1.0.2; scaff10X v. git 4.28.2018; Bionano Solve B spQI/BssSI v. 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; purge_haplotigs v. bit 7.10.2018 Assembly Name :: mPhyDis1.alti.v3 Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 65.8x Sequencing Technology :: PacBio Sequel; 10X Genomics linked reads; Bioanano Genomics 2 enzyme; Arima Genomics HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..10857 /organism="Phyllostomus discolor" /mol_type="genomic DNA" /isolate="MPI-MPIP mPhyDis1" /db_xref="taxon:89673" /sex="male" /tissue_type="muscle" /country="Germany: Munich, Collected from captive colony, LMU" /collection_date="25-Oct-2016" /collected_by="Pedro Rodenas-Cuadrado, Uwe Firzlaff, Sonja Vernes" WGS RXPB02000001-RXPB02010857 // LOCUS RXPA02000000 78 rc DNA linear MAM 11-AUG-2021 DEFINITION Phyllostomus discolor isolate MPI-MPIP mPhyDis1, whole genome shotgun sequencing project. ACCESSION RXPA00000000 VERSION RXPA00000000.2 DBLINK BioProject: PRJNA489141 BioSample: SAMN09948786 KEYWORDS WGS. SOURCE Phyllostomus discolor (pale spear-nosed bat) ORGANISM Phyllostomus discolor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Phyllostomidae; Phyllostominae; Phyllostomus. REFERENCE 1 (bases 1 to 78) AUTHORS Jebb,D., Huang,Z., Pippel,M., Hughes,G.M., Lavrichenko,K., Devanna,P., Winkler,S., Jermiin,L.S., Skirmuntt,E.C., Katzourakis,A., Burkitt-Gray,L., Ray,D.A., Sullivan,K.A.M., Roscito,J.G., Kirilenko,B.M., Davalos,L.M., Corthals,A.P., Power,M.L., Jones,G., Ransome,R.D., Dechmann,D.K.N., Locatelli,A.G., Puechmaille,S.J., Fedrigo,O., Jarvis,E.D., Hiller,M., Vernes,S.C., Myers,E.W. and Teeling,E.C. TITLE Six reference-quality genomes reveal evolution of bat adaptations JOURNAL Nature 583 (7817), 578-584 (2020) PUBMED 32699395 REFERENCE 2 (bases 1 to 78) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 78) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 78) AUTHORS Vernes,S., Fedrigo,O., Teeling,E., Myers,G., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (17-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 78) AUTHORS Vernes,S., Fedrigo,O., Teeling,E., Myers,G., Mountcastle,J., Haase,B., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Formenti,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (05-MAY-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On May 11, 2020 this sequence version replaced RXPA00000000.1. The Phyllostomus discolor whole genome shotgun (WGS) project has the project accession RXPA00000000. This version of the project (02) has the accession number RXPA02000000, and consists of sequences RXPA02000001-RXPA02000078. This assembly represents the principal haplotype of the diploid genome Phyllostomus discolor and includes the chromosomes. The alternate haplotype sequences are in WGS project RXPB00000000. ##Genome-Assembly-Data-START## Assembly Date :: 29-NOV-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; scaff10X v. git 4.28.2018; Bionano Solve B v. spQI/BssSI 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; purge_haplotigs v. bit 7.10.2018; gEVAL manual curation v. 2019-11-29 Assembly Name :: mPhyDis1.pri.v3 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 65.8x Sequencing Technology :: PacBio Sequel; 10X Genomics linked reads; Bioanano Genomics 2 enzyme; Arima Genomics HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..78 /organism="Phyllostomus discolor" /mol_type="genomic DNA" /isolate="MPI-MPIP mPhyDis1" /db_xref="taxon:89673" /sex="male" /tissue_type="muscle" /country="Germany: Munich, Collected from captive colony, LMU" /collection_date="25-Oct-2016" /collected_by="Pedro Rodenas-Cuadrado, Uwe Firzlaff, Sonja Vernes" WGS RXPA02000001-RXPA02000078 WGS_SCAFLD CM014254-CM014268 WGS_SCAFLD CM016611 WGS_SCAFLD CM023025-CM023026 // LOCUS RZJU02000000 5843 rc DNA linear MAM 11-AUG-2021 DEFINITION Ornithorhynchus anatinus isolate Pmale09, whole genome shotgun sequencing project. ACCESSION RZJU00000000 VERSION RZJU00000000.2 DBLINK BioProject: PRJNA489115 BioSample: SAMN08537700 KEYWORDS WGS. SOURCE Ornithorhynchus anatinus (platypus) ORGANISM Ornithorhynchus anatinus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Monotremata; Ornithorhynchidae; Ornithorhynchus. REFERENCE 1 (bases 1 to 5843) AUTHORS Zhou,Y., Shearwin-Whyatt,L., Li,J., Song,Z., Hayakawa,T., Stevens,D., Fenelon,J.C., Peel,E., Cheng,Y., Pajpach,F., Bradley,N., Suzuki,H., Nikaido,M., Damas,J., Daish,T., Perry,T., Zhu,Z., Geng,Y., Rhie,A., Sims,Y., Wood,J., Haase,B., Mountcastle,J., Fedrigo,O., Li,Q., Yang,H., Wang,J., Johnston,S.D., Phillippy,A.M., Howe,K., Jarvis,E.D., Ryder,O.A., Kaessmann,H., Donnelly,P., Korlach,J., Lewin,H.A., Graves,J., Belov,K., Renfree,M.B., Grutzner,F., Zhou,Q. and Zhang,G. TITLE Platypus and echidna genomes reveal mammalian biology and evolution JOURNAL Nature 592 (7856), 756-762 (2021) PUBMED 33408411 REFERENCE 2 (bases 1 to 5843) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 5843) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 5843) AUTHORS Zhang,G., Zhou,Y., Grultzner,F., Zhou,Q., Jarvis,E.D., Fedrigo,O., Howard,J., Korlach,J., Rhie,A., Howe,K., Woods,J., Damas,J., Lewin,H., Durbin,R. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (14-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 5843) AUTHORS Zhang,G., Zhou,Y., Grultzner,F., Zhou,Q., Jarvis,E.D., Fedrigo,O., Howard,J., Korlach,J., Rhie,A., Howe,K., Woods,J., Lewin,H., Durbin,R., Formenti,G. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (09-MAR-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 6, 2020 this sequence version replaced RZJU00000000.1. The Ornithorhynchus anatinus whole genome shotgun (WGS) project has the project accession RZJU00000000. This version of the project (02) has the accession number RZJU02000000, and consists of sequences RZJU02000001-RZJU02005843. This assembly represents the alternate haplotype of the diploid genome Ornithorhynchus anatinus. The principal haplotype sequences are in WGS project RZJT00000000. ##Genome-Assembly-Data-START## Assembly Date :: 06-DEC-2019 Assembly Method :: FALCON v. 5.1.1; FALCON Unzip v. 1.0.2; purge_haplotigs v. bit 7.10.2018; scaff10X v. git 4.28.2018; Bionano Solve DLS v. 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0 Assembly Name :: mOrnAna1.alt.v3 Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 58.8x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads; Bionano Genomics DLS; Dovetail Genomics HiC; Arima Genomics ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..5843 /organism="Ornithorhynchus anatinus" /mol_type="genomic DNA" /isolate="Pmale09" /db_xref="taxon:9258" /sex="male" /tissue_type="liver; muscle" WGS RZJU02000001-RZJU02005843 // LOCUS RZJT02000000 322 rc DNA linear MAM 11-AUG-2021 DEFINITION Ornithorhynchus anatinus isolate Pmale09, whole genome shotgun sequencing project. ACCESSION RZJT00000000 VERSION RZJT00000000.2 DBLINK BioProject: PRJNA489114 BioSample: SAMN08537700 KEYWORDS WGS. SOURCE Ornithorhynchus anatinus (platypus) ORGANISM Ornithorhynchus anatinus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Monotremata; Ornithorhynchidae; Ornithorhynchus. REFERENCE 1 (bases 1 to 322) AUTHORS Zhou,Y., Shearwin-Whyatt,L., Li,J., Song,Z., Hayakawa,T., Stevens,D., Fenelon,J.C., Peel,E., Cheng,Y., Pajpach,F., Bradley,N., Suzuki,H., Nikaido,M., Damas,J., Daish,T., Perry,T., Zhu,Z., Geng,Y., Rhie,A., Sims,Y., Wood,J., Haase,B., Mountcastle,J., Fedrigo,O., Li,Q., Yang,H., Wang,J., Johnston,S.D., Phillippy,A.M., Howe,K., Jarvis,E.D., Ryder,O.A., Kaessmann,H., Donnelly,P., Korlach,J., Lewin,H.A., Graves,J., Belov,K., Renfree,M.B., Grutzner,F., Zhou,Q. and Zhang,G. TITLE Platypus and echidna genomes reveal mammalian biology and evolution JOURNAL Nature 592 (7856), 756-762 (2021) PUBMED 33408411 REFERENCE 2 (bases 1 to 322) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 322) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 322) AUTHORS Zhang,G., Zhou,Y., Grultzner,F., Zhou,Q., Jarvis,E.D., Fedrigo,O., Howard,J., Korlach,J., Rhie,A., Howe,K., Woods,J., Lewin,H., Durbin,R. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (18-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 322) AUTHORS Zhang,G., Zhou,Y., Grultzner,F., Zhou,Q., Jarvis,E.D., Fedrigo,O., Howard,J., Korlach,J., Rhie,A., Howe,K., Woods,J., Lewin,H., Durbin,R., Formenti,G. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (09-MAR-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 6, 2020 this sequence version replaced RZJT00000000.1. The Ornithorhynchus anatinus whole genome shotgun (WGS) project has the project accession RZJT00000000. This version of the project (02) has the accession number RZJT02000000, and consists of sequences RZJT02000001-RZJT02000322. This assembly represents the principal haplotype of the diploid genome Ornithorhynchus anatinus and includes the chromosomes. The alternate haplotype sequences are in WGS project RZJU00000000. ##Genome-Assembly-Data-START## Assembly Date :: 06-DEC-2019 Assembly Method :: FALCON v. 5.1.1; FALCON Unzip v. 1.0.2; purge_haplotigs v. bit 7.10.2018; scaff10X v. git 4.28.2018; Bionano Solve DLS v. 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap fillingt v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-12-06 Assembly Name :: mOrnAna1.pri.v4 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 58.8x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads; Bionano Genomics DLS; Dovetail Genomics HiC; Arima Genomics ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..322 /organism="Ornithorhynchus anatinus" /mol_type="genomic DNA" /isolate="Pmale09" /db_xref="taxon:9258" /sex="male" /tissue_type="liver; muscle" WGS RZJT02000001-RZJT02000322 WGS_SCAFLD CM014200-CM014225 WGS_SCAFLD CM016609 WGS_SCAFLD CM022557-CM022558 WGS_SCAFLD CM026824-CM026826 // LOCUS STFU02000000 541 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Blue55, whole genome shotgun sequencing project. ACCESSION STFU00000000 VERSION STFU00000000.2 DBLINK BioProject: PRJNA489186 BioSample: SAMN09946140 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 541) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 541) AUTHORS Zhang,G., Rahbek,C., Graves,G.R., Lei,F., Jarvis,E.D. and Gilbert,M.T. TITLE Genomics: Bird sequencing project takes off JOURNAL Nature 522 (7554), 34 (2015) PUBMED 26040883 REFERENCE 3 (bases 1 to 541) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 4 (bases 1 to 541) AUTHORS Jarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (12-APR-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 541) AUTHORS Jarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (09-MAR-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Mar 27, 2020 this sequence version replaced STFU00000000.1. The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession STFU00000000. This version of the project (02) has the accession number STFU02000000, and consists of sequences STFU02000001-STFU02000541. This assembly represents the principal haplotype of the diploid genome Taeniopygia guttata and includes the chromosomes. The alternate haplotype sequences are in WGS project STFT00000000. ##Genome-Assembly-Data-START## Assembly Date :: 12-NOV-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; scaff10x v. 2.1; Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-11-12; VGP standard assembly pipeline v. 1.0 Assembly Name :: bTaeGut2.pri.v2 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 101.2x Sequencing Technology :: PacBio Sequel I; 10X genome; Bionano Genomics; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..541 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Blue55" /db_xref="taxon:59729" /sex="female" /tissue_type="Muscle, blood, brain" /dev_stage="adult" /country="USA" /lat_lon="36.0014 N 78.9382 W" /collected_by="Matt Biegler, Duke University and Rockefeller University" WGS STFU02000001-STFU02000541 WGS_SCAFLD CM020832-CM020863 WGS_SCAFLD CM020865 // LOCUS VOHI02000000 205 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Blue55, whole genome shotgun sequencing project. ACCESSION VOHI00000000 VERSION VOHI00000000.2 DBLINK BioProject: PRJNA555095 BioSample: SAMN09946140 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 205) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 205) AUTHORS Jarvis,E.D., Rhie,A., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (10-SEP-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 205) AUTHORS Jarvis,E.D., Rhie,A., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (06-FEB-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Feb 10, 2020 this sequence version replaced VOHI00000000.1. The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession VOHI00000000. This version of the project (02) has the accession number VOHI02000000, and consists of sequences VOHI02000001-VOHI02000205. This assembly represents the principal haplotype of the diploid genome Taeniopygia guttata. This is the VGP 1.5 trio assembly merged haplotype data and includes the chromosomes from the male as well as the female W chromosome and the mitochondrion. The alternate maternal and paternal haplotype sequences are in WGS projects VOHG00000000 and VOHH00000000 respectively. ##Genome-Assembly-Data-START## Assembly Date :: 24-JAN-2020 Assembly Method :: TrioCanu v. 1.7; Scaff10x 2.1 v. git 4.28.2018; Bionano Solve 2 enzyme v. 3.2.1; Salsa v. 2.2; Arrow v. 5.1.0.26412; gEVAL manual curation v. 2019-11-12; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; VGP Trio binning assembly pipeline v. 1.0 Assembly Name :: bTaeGut2.pat.W.v2 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 82.5x Sequencing Technology :: PacBio Sequel I; 10X Genomics chromium; Bionano Genomics 2 enzyme; Arima Genomics Hi-C; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..205 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Blue55" /db_xref="taxon:59729" /sex="female" /tissue_type="Muscle, blood, brain" /dev_stage="adult" /country="USA" /lat_lon="36.0014 N 78.9382 W" /collected_by="Matt Biegler, Duke University and Rockefeller University" WGS VOHI02000001-VOHI02000205 WGS_SCAFLD CM018229-CM018260 WGS_SCAFLD CM021175 // LOCUS VOHG03000000 206 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Blue55, whole genome shotgun sequencing project. ACCESSION VOHG00000000 VERSION VOHG00000000.3 DBLINK BioProject: PRJNA489100 BioSample: SAMN09946140 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 206) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 206) AUTHORS Zhang,G., Rahbek,C., Graves,G.R., Lei,F., Jarvis,E.D. and Gilbert,M.T. TITLE Genomics: Bird sequencing project takes off JOURNAL Nature 522 (7554), 34 (2015) PUBMED 26040883 REFERENCE 3 (bases 1 to 206) AUTHORS Koren,S., Rhie,A., Walenz,B.P., Dilthey,A.T., Bickhart,D.M., Kingan,S.B., Hiendleder,S., Williams,J.L., Smith,T.P.L. and Phillippy,A.M. TITLE Complete assembly of parental haplotypes with trio binning JOURNAL bioRxiv (2018) In press REMARK DOI: 10.1101/271486 REFERENCE 4 (bases 1 to 206) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 5 (bases 1 to 206) AUTHORS Jarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (14-AUG-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 6 (bases 1 to 206) AUTHORS Jarvis,E.D., Rhie,A., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (06-FEB-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Feb 10, 2020 this sequence version replaced VOHG00000000.2. The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession VOHG00000000. This version of the project (03) has the accession number VOHG03000000, and consists of sequences VOHG03000001-VOHG03000206. This assembly represents the maternal alternate haplotype of the diploid genome Taeniopygia guttata. The principal haplotype sequences of the VGP 1.5 trio assembly merged haplotype data are in WGS project VOHI00000000. The paternal alternate haploid sequences are in WGS project VOHH00000000. ##Genome-Assembly-Data-START## Assembly Date :: 24-JAN-2020 Assembly Method :: TrioCanu v. 1.7; Scaff10x v. 2.1 git 4.28.2018; Bionano Solve 2 enzyme v. 3.2.1; Salsa v. 2.2; Arrow v. 5.1.0.26412; gEVAL manual curation v. 2019-11-08; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; VGP Trio binning assembly pipeline v. 1.0 Assembly Name :: bTaeGut2.mat.v3 Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 82.5x Sequencing Technology :: PacBio Sequel I; 10X Genomics chromium; Bionano Genomics 2 enzyme; Arima Genomics Hi-C; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..206 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Blue55" /db_xref="taxon:59729" /sex="female" /tissue_type="Muscle, blood, brain" /dev_stage="adult" /country="USA" /lat_lon="36.0014 N 78.9382 W" /collected_by="Matt Biegler, Duke University and Rockefeller University" WGS VOHG03000001-VOHG03000206 WGS_SCAFLD CM018261-CM018288 WGS_SCAFLD CM018802-CM018805 // LOCUS STFT01000000 4677 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Blue55, whole genome shotgun sequencing project. ACCESSION STFT00000000 VERSION STFT00000000.1 DBLINK BioProject: PRJNA489187 BioSample: SAMN09946140 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 4677) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 4677) AUTHORS Zhang,G., Rahbek,C., Graves,G.R., Lei,F., Jarvis,E.D. and Gilbert,M.T. TITLE Genomics: Bird sequencing project takes off JOURNAL Nature 522 (7554), 34 (2015) PUBMED 26040883 REFERENCE 3 (bases 1 to 4677) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 4 (bases 1 to 4677) AUTHORS Jarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (12-APR-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession STFT00000000. This version of the project (01) has the accession number STFT01000000, and consists of sequences STFT01000001-STFT01004677. This assembly represents the alternate haplotype of the diploid genome Taeniopygia guttata. The principal haplotype sequences are in WGS project STFU00000000. ##Genome-Assembly-Data-START## Assembly Date :: 19-OCT-2018 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. 1.0.2; smrtanalysis Arrow polishing v. 5.1.026412; purge_haplotigs bit v. 7.10.2018; gEVAL manual curation v. 10.19.2018 Assembly Name :: bTaeGut2.p.v1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 82.5x Sequencing Technology :: PacBio Sequel I ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..4677 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Blue55" /db_xref="taxon:59729" /sex="female" /tissue_type="Muscle, blood, brain" /dev_stage="adult" /country="USA" /lat_lon="36.0014 N 78.9382 W" /collected_by="Matt Biegler, Duke University and Rockefeller University" WGS STFT01000001-STFT01004677 // LOCUS RXXE02000000 90 rc DNA linear VRT 11-AUG-2021 DEFINITION Strigops habroptila isolate Jane, whole genome shotgun sequencing project. ACCESSION RXXE00000000 VERSION RXXE00000000.2 DBLINK BioProject: PRJNA489135 BioSample: SAMN09948751 KEYWORDS WGS. SOURCE Strigops habroptila (Kakapo) ORGANISM Strigops habroptila Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Psittaciformes; Psittacidae; Strigops. REFERENCE 1 (bases 1 to 90) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 90) AUTHORS Jarvis,E.D., Howard,J., Rhie,A., Phillippy,A., Korlach,J., Digby,A., Iorns,D., Eason,D., Robertson,B., Raemaekers,T., Howe,K., Lewin,H., Damas,J., Hastie,A. and Fedrigo,O. TITLE Direct Submission JOURNAL Submitted (17-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 90) AUTHORS Jarvis,E.D., Howard,J., Rhie,A., Phillippy,A., Korlach,J., Digby,A., Iorns,D., Eason,D., Robertson,B., Raemaekers,T., Howe,K., Lewin,H., Damas,J., Hastie,A., Tracey,A., Chow,W. and Fedrigo,O. TITLE Direct Submission JOURNAL Submitted (24-NOV-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Dec 27, 2019 this sequence version replaced RXXE00000000.1. The Strigops habroptila whole genome shotgun (WGS) project has the project accession RXXE00000000. This version of the project (02) has the accession number RXXE02000000, and consists of sequences RXXE02000001-RXXE02000090. The chromosome names were updated in August 2019 when the sex chromosomes were identified. Former chromosome 3 is chromosome Z, former chromosome 13 is chromosome W, and the remaining former chromosomes 3-26 were renamed sequentially to chromosomes 4-24 (4-12 are now 3-11, and 14-26 are now 12-24, respectively). This is an updated assembly of GCA_004027225.1. New Hi-C mapping tools (HiGlass) and experience of the VGP with bird genomes were used to re-curate the assembly (using gEVAL), where nearly all previously unlocalized scaffolds are now assembled into their respective chromosomes This assembly represents the principal haplotype of the diploid genome Strigops habroptila and includes the chromosomes. The alternate haplotype sequences are in WGS project RXXF00000000. ##Genome-Assembly-Data-START## Assembly Date :: 08-NOV-2019 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. 1.0.2; scaff10X v. git 4.28.2018; Bionano Solve DLS v. 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; purge_haplotigs v. bit 7.10.2018; gEVAL manual curation v. 2019-11-08 Assembly Name :: bStrHab1.2.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 76.1x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..90 /organism="Strigops habroptila" /mol_type="genomic DNA" /isolate="Jane" /db_xref="taxon:2489341" /sex="female" /tissue_type="blood in lysis buffer or EtOH" /country="New Zealand: Anchor Island" /lat_lon="45.757406 S 166.504927 E" /collection_date="2013-04-13" /collected_by="Tim Raemaekers, Daryl Eason, Andrew Digby of Department of Conservation, New Zealand" WGS RXXE02000001-RXXE02000090 WGS_SCAFLD CM013761-CM013785 WGS_SCAFLD CM013787 // LOCUS VOHH01000000 202 rc DNA linear VRT 11-AUG-2021 DEFINITION Taeniopygia guttata isolate Blue55, whole genome shotgun sequencing project. ACCESSION VOHH00000000 VERSION VOHH00000000.1 DBLINK BioProject: PRJNA489101 BioSample: SAMN09946140 KEYWORDS WGS. SOURCE Taeniopygia guttata (zebra finch) ORGANISM Taeniopygia guttata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia. REFERENCE 1 (bases 1 to 202) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 202) AUTHORS Zhang,G., Rahbek,C., Graves,G.R., Lei,F., Jarvis,E.D. and Gilbert,M.T. TITLE Genomics: Bird sequencing project takes off JOURNAL Nature 522 (7554), 34 (2015) PUBMED 26040883 REFERENCE 3 (bases 1 to 202) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 4 (bases 1 to 202) AUTHORS Jarvis,E.D., Rhie,A., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V. and Phillippy,A. TITLE Direct Submission JOURNAL Submitted (10-SEP-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession VOHH00000000. This version of the project (01) has the accession number VOHH01000000, and consists of sequences VOHH01000001-VOHH01000202. This assembly represents the paternal alternate haplotype of the diploid genome Taeniopygia guttata. The principal haplotype sequences of the VGP 1.5 trio assembly merged haplotype data are in WGS project VOHI00000000. The maternal alternate haploid sequences are in WGS project VOHG00000000. The bTaeGut2p assembly is based on the VGP 1.5 trio binning pipeline. Initial PacBio read binning into maternal and paternal haplotypes using parental Illumina short reads. Then each haplotype is assembled into contigs with Canu, followed by 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Bionano Solve, Hi-C based scaffolding with SALSA2, Arrow polishing and gap filling, and two rounds of FreeBayes polishing with Illumina short reads. This assembly was curated with chromosomes annotated using gEVAL before the FreeBayes polishing. ##Genome-Assembly-Data-START## Assembly Date :: 21-AUG-2019 Assembly Method :: Trio Binning v. 1; Canu v. 1.7; Scaff10x v. 2.1(git 4.28.2018); Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; gEVAL manual curation v. 2019-05-24; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.2.0; VGP Trio binning assembly pipeline v. 1.5 Assembly Name :: bTaeGut2pat Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 82.5x Sequencing Technology :: PacBio Sequel; 10X genome; Bionano Genomics; Arima Genomics Hi-C; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..202 /organism="Taeniopygia guttata" /mol_type="genomic DNA" /isolate="Blue55" /db_xref="taxon:59729" /sex="female" /tissue_type="Muscle, blood, brain" /dev_stage="adult" /country="USA" /lat_lon="36.0014 N 78.9382 W" /collected_by="Matt Biegler, Duke University and Rockefeller University" WGS VOHH01000001-VOHH01000202 WGS_SCAFLD CM018289-CM018318 // LOCUS VHHO01000000 8736 rc DNA linear VRT 11-AUG-2021 DEFINITION Gopherus evgoodei, whole genome shotgun sequencing project. ACCESSION VHHO00000000 VERSION VHHO00000000.1 DBLINK BioProject: PRJNA489104 BioSample: SAMN03496275 KEYWORDS WGS. SOURCE Gopherus evgoodei (Goodes thornscrub tortoise) ORGANISM Gopherus evgoodei Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Testudinoidea; Testudinidae; Gopherus. REFERENCE 1 (bases 1 to 8736) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 8736) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 8736) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 8736) AUTHORS Murphy,B., Edwards,T., Rhie,A., Koren,S., Phillippy,A., Fedrigo,O., Haase,B., Mountcastle,J., Lewin,H., Damas,J., Howe,K., Formenti,G., Myers,G., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (13-MAY-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Gopherus evgoodei whole genome shotgun (WGS) project has the project accession VHHO00000000. This version of the project (01) has the accession number VHHO01000000, and consists of sequences VHHO01000001-VHHO01008736. This assembly represents the alternate haplotype of the diploid genome Gopherus evgoodei. The principal haplotype sequences are in WGS project VHHN00000000. ##Genome-Assembly-Data-START## Assembly Date :: 31-JAN-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; purge_haplotigs v. bitbucket 7.10.2018; scaff10x v. 2.1; Bionano Solve DLS v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-01-31; VGP standard assembly pipeline v. 1.5 Assembly Name :: rGopEvg1_v1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 58.0x Sequencing Technology :: PacBio Sequel I; 10X Genomics linked reads; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..8736 /organism="Gopherus evgoodei" /mol_type="genomic DNA" /db_xref="taxon:1825980" /sex="male" /tissue_type="whole blood" /ecotype="Sinaloan lineage" /country="Mexico: Sonora" /collection_date="2010-08-10" /collected_by="T. Edwards" WGS VHHO01000001-VHHO01008736 // LOCUS VHHN01000000 383 rc DNA linear VRT 11-AUG-2021 DEFINITION Gopherus evgoodei, whole genome shotgun sequencing project. ACCESSION VHHN00000000 VERSION VHHN00000000.1 DBLINK BioProject: PRJNA489103 BioSample: SAMN03496275 KEYWORDS WGS. SOURCE Gopherus evgoodei (Goodes thornscrub tortoise) ORGANISM Gopherus evgoodei Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Testudinoidea; Testudinidae; Gopherus. REFERENCE 1 (bases 1 to 383) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 383) AUTHORS Murphy,B., Edwards,T., Rhie,A., Koren,S., Phillippy,A., Fedrigo,O., Haase,B., Mountcastle,J., Lewin,H., Damas,J., Howe,K., Formenti,G., Myers,G., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-JUN-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Gopherus evgoodei whole genome shotgun (WGS) project has the project accession VHHN00000000. This version of the project (01) has the accession number VHHN01000000, and consists of sequences VHHN01000001-VHHN01000383. This assembly represents the principal haplotype of the diploid genome Gopherus evgoodei and includes the chromosomes. The alternate haplotype sequences are in WGS project VHHO00000000. ##Genome-Assembly-Data-START## Assembly Date :: 31-JAN-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; purge_haplotigs v. bitbucket 7.10.2018; scaff10x v. 2.1; Bionano Solve DLS v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-01-31; VGP standard assembly pipeline v. 1.5 Assembly Name :: rGopEvg1_v1.p Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 58.0x Sequencing Technology :: PacBio Sequel I; 10X Genomics linked reads; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..383 /organism="Gopherus evgoodei" /mol_type="genomic DNA" /db_xref="taxon:1825980" /sex="male" /tissue_type="whole blood" /ecotype="Sinaloan lineage" /country="Mexico: Sonora" /collection_date="2010-08-10" /collected_by="T. Edwards" WGS VHHN01000001-VHHN01000383 WGS_SCAFLD CM017296-CM017320 // LOCUS STFW01000000 9292 rc DNA linear VRT 11-AUG-2021 DEFINITION Archocentrus centrarchus isolate MPI-CPG fArcCen1, whole genome shotgun sequencing project. ACCESSION STFW00000000 VERSION STFW00000000.1 DBLINK BioProject: PRJNA489130 BioSample: SAMN09948522 KEYWORDS WGS. SOURCE Archocentrus centrarchus (flier cichlid) ORGANISM Archocentrus centrarchus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae; New World cichlids; Cichlasomatinae; Heroini; Archocentrus. REFERENCE 1 (bases 1 to 9292) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 9292) AUTHORS Jebb,D., Huang,Z., Pippel,M., Hughes,G.M., Lavrichenko,K., Devanna,P., Winkler,S., Jermiin,L.S., Skirmuntt,E.C., Katzourakis,A., Burkitt-Gray,L., Ray,D.A., Sullivan,K.A.M., Roscito,J.G., Kirilenko,B.M., Davalos,L.M., Corthals,A.P., Power,M.L., Jones,G., Ransome,R.D., Dechmann,D.K.N., Locatelli,A.G., Puechmaille,S.J., Fedrigo,O., Jarvis,E.D., Hiller,M., Vernes,S.C., Myers,E.W. and Teeling,E.C. TITLE Six reference-quality genomes reveal evolution of bat adaptations JOURNAL Nature 583 (7817), 578-584 (2020) PUBMED 32699395 REFERENCE 3 (bases 1 to 9292) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 4 (bases 1 to 9292) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 5 (bases 1 to 9292) AUTHORS Myers,G., Meyer,A., Pippel,M., Winkler,S., Formenti,G., Fedrigo,O., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Mountcastle,J., Mccarthy,S., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (12-APR-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Archocentrus centrarchus whole genome shotgun (WGS) project has the project accession STFW00000000. This version of the project (01) has the accession number STFW01000000, and consists of sequences STFW01000001-STFW01009292. This assembly represents the alternate haplotype of the diploid genome Archocentrus centrarchus. The principal haplotype sequences are in WGS project STFV00000000. ##Genome-Assembly-Data-START## Assembly Date :: 08-FEB-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; scaff10x v. 2.1; Bionano Solve DLS v. 3.2.1; Salsa2 v. 2.0; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-02-08; VGP standard assembly pipeline v. 1.0 Assembly Name :: fArcCen1_v1.h Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 76.0x Sequencing Technology :: PacBio Sequel I; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..9292 /organism="Archocentrus centrarchus" /mol_type="genomic DNA" /isolate="MPI-CPG fArcCen1" /db_xref="taxon:63155" /sex="male" /tissue_type="muscle" /country="Nicaragua" /lat_lon="12.8654 N 85.2072 W" /collection_date="2016-03-09" /collected_by="Axel Meyer, Andreas Kautt, Paolo Franchini" WGS STFW01000001-STFW01009292 // LOCUS STFV01000000 189 rc DNA linear VRT 11-AUG-2021 DEFINITION Archocentrus centrarchus isolate MPI-CPG fArcCen1, whole genome shotgun sequencing project. ACCESSION STFV00000000 VERSION STFV00000000.1 DBLINK BioProject: PRJNA489129 BioSample: SAMN09948522 KEYWORDS WGS. SOURCE Archocentrus centrarchus (flier cichlid) ORGANISM Archocentrus centrarchus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae; New World cichlids; Cichlasomatinae; Heroini; Archocentrus. REFERENCE 1 (bases 1 to 189) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 2 (bases 1 to 189) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 189) AUTHORS Myers,G., Meyer,A., Pippel,M., Winkler,S., Formenti,G., Fedrigo,O., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Mountcastle,J., Mccarthy,S., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (12-APR-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Archocentrus centrarchus whole genome shotgun (WGS) project has the project accession STFV00000000. This version of the project (01) has the accession number STFV01000000, and consists of sequences STFV01000001-STFV01000189. This assembly represents the principal haplotype of the diploid genome Archocentrus centrarchus and includes the chromosomes. The alternate haplotype sequences are in WGS project STFW00000000. ##Genome-Assembly-Data-START## Assembly Date :: 08-FEB-2019 Assembly Method :: FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; scaff10x v. 2.1; Bionano Solve DLS v. 3.2.1; Salsa2 v. 2.0; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-02-08; VGP standard assembly pipeline v. 1.0 Assembly Name :: fArcCen1 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 76.0x Sequencing Technology :: PacBio Sequel I; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..189 /organism="Archocentrus centrarchus" /mol_type="genomic DNA" /isolate="MPI-CPG fArcCen1" /db_xref="taxon:63155" /sex="male" /tissue_type="muscle" /country="Nicaragua" /lat_lon="12.8654 N 85.2072 W" /collection_date="2016-03-09" /collected_by="Axel Meyer, Andreas Kautt, Paolo Franchini" WGS STFV01000001-STFV01000189 WGS_SCAFLD CM017272-CM017295 WGS_SCAFLD CM017446 // LOCUS RXPC01000000 135 rc DNA linear MAM 11-AUG-2021 DEFINITION Rhinolophus ferrumequinum isolate MPI-CBG mRhiFer1, whole genome shotgun sequencing project. ACCESSION RXPC00000000 VERSION RXPC00000000.1 DBLINK BioProject: PRJNA489106 BioSample: SAMN09948510 KEYWORDS WGS. SOURCE Rhinolophus ferrumequinum (greater horseshoe bat) ORGANISM Rhinolophus ferrumequinum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus. REFERENCE 1 (bases 1 to 135) AUTHORS Jebb,D., Huang,Z., Pippel,M., Hughes,G.M., Lavrichenko,K., Devanna,P., Winkler,S., Jermiin,L.S., Skirmuntt,E.C., Katzourakis,A., Burkitt-Gray,L., Ray,D.A., Sullivan,K.A.M., Roscito,J.G., Kirilenko,B.M., Davalos,L.M., Corthals,A.P., Power,M.L., Jones,G., Ransome,R.D., Dechmann,D.K.N., Locatelli,A.G., Puechmaille,S.J., Fedrigo,O., Jarvis,E.D., Hiller,M., Vernes,S.C., Myers,E.W. and Teeling,E.C. TITLE Six reference-quality genomes reveal evolution of bat adaptations JOURNAL Nature 583 (7817), 578-584 (2020) PUBMED 32699395 REFERENCE 2 (bases 1 to 135) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 135) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 135) AUTHORS Teeling,E., Myers,G., Vernes,S., Pippel,M., Winkler,S., Fedrigo,O., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Mountcastle,J. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (17-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 5 (bases 1 to 135) AUTHORS Teeling,E., Myers,G., Vernes,S., Pippel,M., Winkler,S., Fedrigo,O., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Mountcastle,J., Jarvis,E.D. and Formenti,G. TITLE Direct Submission JOURNAL Submitted (08-MAY-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On May 16, 2019 this sequence version replaced gi:1562586953. The Rhinolophus ferrumequinum whole genome shotgun (WGS) project has the project accession RXPC00000000. This version of the project (01) has the accession number RXPC01000000, and consists of sequences RXPC01000001-RXPC01000135. This assembly represents the primary haplotype of the diploid genome Rhinolophus ferrumequinum and includes the chromosomes. The alternate haplotype sequences are in WGS project RXPD00000000. In May 2019 the mitochondrial sequence (RXPC01000135) was added to this 01 version of RXPC00000000. In November 2020 chromosome 1 was changed to chromosome X based on read mapping and homology evidence with other species, and the animal's gender was corrected to female. ##Genome-Assembly-Data-START## Assembly Date :: 07-SEP-2018 Assembly Method :: FALCON-Unzip v. 1.0.2; scaff10X v. git 4.28.2018; Bionano Solve v. BspQI/BssSI 3.2.1; Salsa2 v. HiC 2.0; purge_haplotigs v. bit 7.10.2018; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; FALCON v. 5.1.1; freebayes v. 1.2.0; gEVAL manual curation v. 2018-09-07 Assembly Name :: mRhiFer1_v1.p Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 52.8x Sequencing Technology :: PacBio Sequel; 10X Genomics linked reads; Bionano Genomics 2 enzyme; Phase Genomics HiC ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..135 /organism="Rhinolophus ferrumequinum" /mol_type="genomic DNA" /isolate="MPI-CBG mRhiFer1" /db_xref="taxon:59479" /sex="female" /tissue_type="liver" /country="United Kingdom: Woodchester Mansion, Gloucestershire" /lat_lon="51.7108 N 2.2776 W" /collection_date="2016-05-31" /collected_by="Gareth Jones" WGS RXPC01000001-RXPC01000135 WGS_SCAFLD CM014226-CM014253 WGS_SCAFLD CM016610 // LOCUS RXPD01000000 13424 rc DNA linear MAM 11-AUG-2021 DEFINITION Rhinolophus ferrumequinum isolate MPI-CBG mRhiFer1, whole genome shotgun sequencing project. ACCESSION RXPD00000000 VERSION RXPD00000000.1 DBLINK BioProject: PRJNA489105 BioSample: SAMN09948510 KEYWORDS WGS. SOURCE Rhinolophus ferrumequinum (greater horseshoe bat) ORGANISM Rhinolophus ferrumequinum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus. REFERENCE 1 (bases 1 to 13424) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 13424) AUTHORS Teeling,E.C., Vernes,S.C., Davalos,L.M., Ray,D.A., Gilbert,M.T.P. and Myers,E. CONSRTM Bat1K Consortium TITLE Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species JOURNAL Annu Rev Anim Biosci 6, 23-46 (2018) PUBMED 29166127 REFERENCE 3 (bases 1 to 13424) AUTHORS Jebb,D., Huang,Z., Pippel,M., Hughes,G.M., Lavrichenko,K., Devanna,P., Winkler,S., Jermiin,L.S., Skirmuntt,E.C., Katzourakis,A., Burkitt-Gray,L., Ray,D.A., Sullivan,K.A.M., Roscito,J.G., Kirilenko,B.M., Davalos,L.M., Corthals,A.P., Power,M.L., Jones,G., Ransome,R.D., Dechmann,D.K.N., Locatelli,A.G., Puechmaille,S.J., Fedrigo,O., Jarvis,E.D., Hiller,M., Vernes,S.C., Myers,E.W. and Teeling,E.C. TITLE Six reference-quality genomes reveal evolution of bat adaptations JOURNAL Nature 583 (7817), 578-584 (2020) PUBMED 32699395 REFERENCE 4 (bases 1 to 13424) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 5 (bases 1 to 13424) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 6 (bases 1 to 13424) AUTHORS Teeling,E., Myers,G., Vernes,S., Pippel,M., Winkler,S., Fedrigo,O., Rhie,A., Koren,S., Phillippy,A., Lewin,H., Damas,J., Howe,K., Mountcastle,J. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (17-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Rhinolophus ferrumequinum whole genome shotgun (WGS) project has the project accession RXPD00000000. This version of the project (01) has the accession number RXPD01000000, and consists of sequences RXPD01000001-RXPD01013424. This assembly represents the alternate haplotype of the diploid genome Rhinolophus ferrumequinum. The primary haplotype sequences are in WGS project RXPC00000000. ##Genome-Assembly-Data-START## Assembly Date :: 07-SEP-2018 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. 1.0.2; purge_haplotigs v. bit 7.10.2018; smrtanalysis Arrow polishing v. 5.1.0.26412; gEVAL manual curation v. 2018-09-07 Assembly Name :: mRhiFer1_v1.h Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 52.8x Sequencing Technology :: PacBio Sequel; 10X Genomics linked reads ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..13424 /organism="Rhinolophus ferrumequinum" /mol_type="genomic DNA" /isolate="MPI-CBG mRhiFer1" /db_xref="taxon:59479" /sex="female" /tissue_type="liver" /country="United Kingdom: Woodchester Mansion, Gloucestershire" /lat_lon="51.7108 N 2.2776 W" /collection_date="2016-05-31" /collected_by="Gareth Jones" WGS RXPD01000001-RXPD01013424 // LOCUS RXXF01000000 3728 rc DNA linear VRT 11-AUG-2021 DEFINITION Strigops habroptila isolate Jane, whole genome shotgun sequencing project. ACCESSION RXXF00000000 VERSION RXXF00000000.1 DBLINK BioProject: PRJNA489134 BioSample: SAMN09948751 KEYWORDS WGS. SOURCE Strigops habroptila (Kakapo) ORGANISM Strigops habroptila Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Psittaciformes; Psittacidae; Strigops. REFERENCE 1 (bases 1 to 3728) AUTHORS Koepfli,K.P., Paten,B. and O'Brien,S.J. CONSRTM Genome 10K Community of Scientists TITLE The Genome 10K Project: a way forward JOURNAL Annu Rev Anim Biosci 3, 57-111 (2015) PUBMED 25689317 REFERENCE 2 (bases 1 to 3728) AUTHORS Rhie,A., McCarthy,S.A., Fedrigo,O., Damas,J., Formenti,G., Koren,S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., Lee,C., Ko,B.J., Chaisson,M., Gedman,G.L., Cantin,L.J., Thibaud-Nissen,F., Haggerty,L., Bista,I., Smith,M., Haase,B., Mountcastle,J., Winkler,S., Paez,S., Howard,J., Vernes,S.C., Lama,T.M., Grutzner,F., Warren,W.C., Balakrishnan,C.N., Burt,D., George,J.M., Biegler,M.T., Iorns,D., Digby,A., Eason,D., Robertson,B., Edwards,T., Wilkinson,M., Turner,G., Meyer,A., Kautt,A.F., Franchini,P., Detrich,H.W. III, Svardal,H., Wagner,M., Naylor,G.J.P., Pippel,M., Malinsky,M., Mooney,M., Simbirsky,M., Hannigan,B.T., Pesout,T., Houck,M., Misuraca,A., Kingan,S.B., Hall,R., Kronenberg,Z., Sovic,I., Dunn,C., Ning,Z., Hastie,A., Lee,J., Selvaraj,S., Green,R.E., Putnam,N.H., Gut,I., Ghurye,J., Garrison,E., Sims,Y., Collins,J., Pelan,S., Torrance,J., Tracey,A., Wood,J., Dagnew,R.E., Guan,D., London,S.E., Clayton,D.F., Mello,C.V., Friedrich,S.R., Lovell,P.V., Osipova,E., Al-Ajli,F.O., Secomandi,S., Kim,H., Theofanopoulou,C., Hiller,M., Zhou,Y., Harris,R.S., Makova,K.D., Medvedev,P., Hoffman,J., Masterson,P., Clark,K., Martin,F., Howe,K., Flicek,P., Walenz,B.P., Kwak,W., Clawson,H., Diekhans,M., Nassar,L., Paten,B., Kraus,R.H.S., Crawford,A.J., Gilbert,M.T.P., Zhang,G., Venkatesh,B., Murphy,R.W., Koepfli,K.P., Shapiro,B., Johnson,W.E., Di Palma,F., Marques-Bonet,T., Teeling,E.C., Warnow,T., Graves,J.M., Ryder,O.A., Haussler,D., O'Brien,S.J., Korlach,J., Lewin,H.A., Howe,K., Myers,E.W., Durbin,R., Phillippy,A.M. and Jarvis,E.D. TITLE Towards complete and error-free genome assemblies of all vertebrate species JOURNAL Nature 592 (7856), 737-746 (2021) PUBMED 33911273 REFERENCE 3 (bases 1 to 3728) AUTHORS Formenti,G., Rhie,A., Balacco,J., Haase,B., Mountcastle,J., Fedrigo,O., Brown,S., Capodiferro,M.R., Al-Ajli,F.O., Ambrosini,R., Houde,P., Koren,S., Oliver,K., Smith,M., Skelton,J., Betteridge,E., Dolucan,J., Corton,C., Bista,I., Torrance,J., Tracey,A., Wood,J., Uliano-Silva,M., Howe,K., McCarthy,S., Winkler,S., Kwak,W., Korlach,J., Fungtammasan,A., Fordham,D., Costa,V., Mayes,S., Chiara,M., Horner,D.S., Myers,E., Durbin,R., Achilli,A., Braun,E.L., Phillippy,A.M. and Jarvis,E.D. CONSRTM Vertebrate Genomes Project Consortium TITLE Complete vertebrate mitogenomes reveal widespread repeats and gene duplications JOURNAL Genome Biol 22 (1), 120 (2021) PUBMED 33910595 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 3728) AUTHORS Jarvis,E.D., Howard,J., Rhie,A., Phillippy,A., Korlach,J., Digby,A., Iorns,D., Eason,D., Robertson,B., Raemaekers,T., Howe,K., Lewin,H., Damas,J., Hastie,A. and Fedrigo,O. TITLE Direct Submission JOURNAL Submitted (15-DEC-2018) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Strigops habroptila whole genome shotgun (WGS) project has the project accession RXXF00000000. This version of the project (01) has the accession number RXXF01000000, and consists of sequences RXXF01000001-RXXF01003728. This assembly represents the alternate haplotype of the diploid genome Strigops habroptila. The primary haplotype sequences are in WGS project RXXE00000000. ##Genome-Assembly-Data-START## Assembly Date :: 07-SEP-2018 Assembly Method :: FALCON v. 5.1.1; FALCON unzip v. 1.0.2; smrtanalysis Arrow polishing v. 5.1.0.26412; purge_haplotigs v. bit 7.10.2018; gEVAL manual curation v. 2018-12-11 Assembly Name :: bStrHab1_v1.h Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 76.1x Sequencing Technology :: PacBio RSII; 10X Genomics linked reads ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..3728 /organism="Strigops habroptila" /mol_type="genomic DNA" /isolate="Jane" /db_xref="taxon:2489341" /sex="female" /tissue_type="blood in lysis buffer or EtOH" /country="New Zealand: Anchor Island" /lat_lon="45.757406 S 166.504927 E" /collection_date="2013-04-13" /collected_by="Tim Raemaekers, Daryl Eason, Andrew Digby of Department of Conservation, New Zealand" WGS RXXF01000001-RXXF01003728 // LOCUS JAHYBR010000000 18 rc DNA linear MAM 03-AUG-2021 DEFINITION Dromiciops gliroides isolate mDroGli1, whole genome shotgun sequencing project. ACCESSION JAHYBR000000000 VERSION JAHYBR000000000.1 DBLINK BioProject: PRJNA728141 BioSample: SAMN18857598 KEYWORDS WGS. SOURCE Dromiciops gliroides (monito del monte) ORGANISM Dromiciops gliroides Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Microbiotheria; Microbiotheriidae; Dromiciops. REFERENCE 1 (bases 1 to 18) AUTHORS Nespolo,R., Quintero,J., Brown,T., Formenti,G., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Saenz-Agudelo,P., Fedrigo,O., Johnson,W., Myers,G. and Jarvis,E.D. TITLE Dromiciops gliroides (monito del monte) genome, mDroGli1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 18) AUTHORS Nespolo,R., Quintero,J., Brown,T., Formenti,G., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Saenz-Agudelo,P., Fedrigo,O., Johnson,W., Myers,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (14-JUL-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Dromiciops gliroides whole genome shotgun (WGS) project has the project accession JAHYBR000000000. This version of the project (01) has the accession number JAHYBR010000000, and consists of sequences JAHYBR010000001-JAHYBR010000018. ##Genome-Assembly-Data-START## Assembly Date :: 07-APR-2021 Assembly Method :: FALCON kit v. 1.8.1; FALCON unzip v. 1.3.7; purge_dups v. 1.2.3; Scaff10X v. 4.2; Bionano Solve v. 3.5.1_01142020; Salsa Hi-C v. 2.2; GCPP v. 1.9.0-SL-release-8.0.0+1-37-gd7b188d; longranger v. 2.2.2; freebayes v. 1.3.2; gEVAL manual curation v. 2021-04-07; VGP pipeline v. 1.6 Assembly Name :: mDroGli1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 63.0x Sequencing Technology :: PacBio Sequel II CLRQ; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics v1 Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..18 /organism="Dromiciops gliroides" /mol_type="genomic DNA" /isolate="mDroGli1" /db_xref="taxon:33562" /sex="female" /tissue_type="kidney, liver" /dev_stage="adult" /country="Chile: San Martin, comuna de Valdivia, Region de los Rios" /lat_lon="39.647794 S 73.196942 W" /collection_date="2014-02-10" /collected_by="Roberto Nespolo, Julian Quintero" WGS JAHYBR010000001-JAHYBR010000018 WGS_SCAFLD CM033365-CM033371 WGS_SCAFLD CM033468 // LOCUS JAHYBS010000000 9926 rc DNA linear MAM 29-JUL-2021 DEFINITION Dromiciops gliroides isolate mDroGli1, whole genome shotgun sequencing project. ACCESSION JAHYBS000000000 VERSION JAHYBS000000000.1 DBLINK BioProject: PRJNA728142 BioSample: SAMN18857598 KEYWORDS WGS. SOURCE Dromiciops gliroides (monito del monte) ORGANISM Dromiciops gliroides Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Microbiotheria; Microbiotheriidae; Dromiciops. REFERENCE 1 (bases 1 to 9926) AUTHORS Nespolo,R., Quintero,J., Brown,T., Formenti,G., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Saenz-Agudelo,P., Fedrigo,O., Johnson,W., Myers,G. and Jarvis,E.D. TITLE Dromiciops gliroides (monito del monte) genome, mDroGli1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 9926) AUTHORS Nespolo,R., Quintero,J., Brown,T., Formenti,G., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Saenz-Agudelo,P., Fedrigo,O., Johnson,W., Myers,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (14-JUL-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Dromiciops gliroides whole genome shotgun (WGS) project has the project accession JAHYBS000000000. This version of the project (01) has the accession number JAHYBS010000000, and consists of sequences JAHYBS010000001-JAHYBS010009926. ##Genome-Assembly-Data-START## Assembly Date :: 07-APR-2021 Assembly Method :: FALCON kit v. 1.8.1; FALCON unzip v. 1.3.7; purge_dups v. 1.2.3; Scaff10X v. 4.2; Bionano Solve v. 3.5.1_01142020; Salsa Hi-C v. 2.2; GCPP v. 1.9.0-SL-release-8.0.0+1-37-gd7b188d; longranger v. 2.2.2; freebayes v. 1.3.2; gEVAL manual curation v. 2021-04-07; VGP pipeline v. 1.6 Assembly Name :: mDroGli1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 63.0x Sequencing Technology :: PacBio Sequel II CLR; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics v1 Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..9926 /organism="Dromiciops gliroides" /mol_type="genomic DNA" /isolate="mDroGli1" /db_xref="taxon:33562" /sex="female" /tissue_type="kidney, liver" /dev_stage="adult" /country="Chile: San Martin, comuna de Valdivia, Region de los Rios" /lat_lon="39.647794 S 73.196942 W" /collection_date="2014-02-10" /collected_by="Roberto Nespolo, Julian Quintero" WGS JAHYBS010000001-JAHYBS010009926 // LOCUS CAJVRZ010000000 60 rc DNA linear INV 28-JUL-2021 DEFINITION Furcula furcula, whole genome shotgun sequencing project. ACCESSION CAJVRZ000000000 VERSION CAJVRZ000000000.1 DBLINK BioProject: PRJEB46629 BioSample: SAMEA7746637 KEYWORDS WGS. SOURCE Furcula furcula ORGANISM Furcula furcula Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Stauropinae; Furcula. REFERENCE 1 (bases 1 to 60) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Furcula furcula whole genome shotgun (WGS) project has the project accession CAJVRZ000000000. This version of the project (01) has the accession number CAJVRZ010000000, and consists of sequences CAJVRZ010000001-CAJVRZ010000060. The assembly ilFurFurc1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..60 /organism="Furcula furcula" /mol_type="genomic DNA" /db_xref="taxon:987943" WGS CAJVRZ010000001-CAJVRZ010000060 // LOCUS CAJVRW010000000 4352 rc DNA linear INV 28-JUL-2021 DEFINITION Pterostichus madidus, whole genome shotgun sequencing project. ACCESSION CAJVRW000000000 VERSION CAJVRW000000000.1 DBLINK BioProject: PRJEB46628 BioSample: SAMEA7520318 KEYWORDS WGS. SOURCE Pterostichus madidus ORGANISM Pterostichus madidus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Caraboidea; Carabidae; Harpalinae; Pterostichini; Pterostichus; Steropus. REFERENCE 1 (bases 1 to 4352) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pterostichus madidus whole genome shotgun (WGS) project has the project accession CAJVRW000000000. This version of the project (01) has the accession number CAJVRW010000000, and consists of sequences CAJVRW010000001-CAJVRW010004352. The assembly icPteMadi1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Some regions of the genome have large repeats with less certain structure than the rest of the assembly, most notably chromosomes 14,15 and 18. Chromosome 14 from 23.8mb onwards has strong Hi-C association with chromosome 18. FEATURES Location/Qualifiers source 1..4352 /organism="Pterostichus madidus" /mol_type="genomic DNA" /db_xref="taxon:767470" WGS CAJVRW010000001-CAJVRW010004352 // LOCUS CAJVRV010000000 50 rc DNA linear INV 28-JUL-2021 DEFINITION Pammene fasciana, whole genome shotgun sequencing project. ACCESSION CAJVRV000000000 VERSION CAJVRV000000000.1 DBLINK BioProject: PRJEB46631 BioSample: SAMEA7701530 KEYWORDS WGS. SOURCE Pammene fasciana ORGANISM Pammene fasciana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Grapholitini; Pammene. REFERENCE 1 (bases 1 to 50) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pammene fasciana whole genome shotgun (WGS) project has the project accession CAJVRV000000000. This version of the project (01) has the accession number CAJVRV010000000, and consists of sequences CAJVRV010000001-CAJVRV010000050. The assembly ilPamFasc1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..50 /organism="Pammene fasciana" /mol_type="genomic DNA" /db_xref="taxon:1101027" WGS CAJVRV010000001-CAJVRV010000050 // LOCUS CAJVRR010000000 1530 rc DNA linear INV 28-JUL-2021 DEFINITION Peribatodes rhomboidaria, whole genome shotgun sequencing project. ACCESSION CAJVRR000000000 VERSION CAJVRR000000000.1 DBLINK BioProject: PRJEB46634 BioSample: SAMEA7701524 KEYWORDS WGS. SOURCE Peribatodes rhomboidaria (willow beauty) ORGANISM Peribatodes rhomboidaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Peribatodes. REFERENCE 1 (bases 1 to 1530) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Peribatodes rhomboidaria whole genome shotgun (WGS) project has the project accession CAJVRR000000000. This version of the project (01) has the accession number CAJVRR010000000, and consists of sequences CAJVRR010000001-CAJVRR010001530. The assembly ilPerRhom1.1 is based on 44x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1530 /organism="Peribatodes rhomboidaria" /mol_type="genomic DNA" /db_xref="taxon:190356" WGS CAJVRR010000001-CAJVRR010001530 // LOCUS CAJVRS010000000 1396 rc DNA linear INV 28-JUL-2021 DEFINITION Marthasterias glacialis, whole genome shotgun sequencing project. ACCESSION CAJVRS000000000 VERSION CAJVRS000000000.1 DBLINK BioProject: PRJEB46623 BioSample: SAMEA7522991 KEYWORDS WGS. SOURCE Marthasterias glacialis (spiny starfish) ORGANISM Marthasterias glacialis Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Asterozoa; Asteroidea; Forcipulatacea; Forcipulatida; Asteriidae; Marthasterias. REFERENCE 1 (bases 1 to 1396) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Marthasterias glacialis whole genome shotgun (WGS) project has the project accession CAJVRS000000000. This version of the project (01) has the accession number CAJVRS010000000, and consists of sequences CAJVRS010000001-CAJVRS010001396. The assembly eaMarGlac1.1 is based on 49x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1396 /organism="Marthasterias glacialis" /mol_type="genomic DNA" /db_xref="taxon:7609" WGS CAJVRS010000001-CAJVRS010001396 // LOCUS CAJVRO010000000 554 rc DNA linear INV 28-JUL-2021 DEFINITION Apoderus coryli, whole genome shotgun sequencing project. ACCESSION CAJVRO000000000 VERSION CAJVRO000000000.1 DBLINK BioProject: PRJEB46625 BioSample: SAMEA7520690 KEYWORDS WGS. SOURCE Apoderus coryli (hazel leaf roller) ORGANISM Apoderus coryli Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Attelabidae; Apoderinae; Apoderus. REFERENCE 1 (bases 1 to 554) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Apoderus coryli whole genome shotgun (WGS) project has the project accession CAJVRO000000000. This version of the project (01) has the accession number CAJVRO010000000, and consists of sequences CAJVRO010000001-CAJVRO010000554. The assembly icApoCory1.1 is based on 59x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..554 /organism="Apoderus coryli" /mol_type="genomic DNA" /db_xref="taxon:201766" WGS CAJVRO010000001-CAJVRO010000554 // LOCUS CAJVRT010000000 84 rc DNA linear INV 28-JUL-2021 DEFINITION Marthasterias glacialis, whole genome shotgun sequencing project. ACCESSION CAJVRT000000000 VERSION CAJVRT000000000.1 DBLINK BioProject: PRJEB46624 BioSample: SAMEA7522991 KEYWORDS WGS. SOURCE Marthasterias glacialis (spiny starfish) ORGANISM Marthasterias glacialis Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Asterozoa; Asteroidea; Forcipulatacea; Forcipulatida; Asteriidae; Marthasterias. REFERENCE 1 (bases 1 to 84) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Marthasterias glacialis whole genome shotgun (WGS) project has the project accession CAJVRT000000000. This version of the project (01) has the accession number CAJVRT010000000, and consists of sequences CAJVRT010000001-CAJVRT010000084. The assembly eaMarGlac1.1 is based on 49x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..84 /organism="Marthasterias glacialis" /mol_type="genomic DNA" /db_xref="taxon:7609" WGS CAJVRT010000001-CAJVRT010000084 // LOCUS CAJVRQ010000000 108 rc DNA linear INV 28-JUL-2021 DEFINITION Apoderus coryli, whole genome shotgun sequencing project. ACCESSION CAJVRQ000000000 VERSION CAJVRQ000000000.1 DBLINK BioProject: PRJEB46626 BioSample: SAMEA7520690 KEYWORDS WGS. SOURCE Apoderus coryli (hazel leaf roller) ORGANISM Apoderus coryli Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Attelabidae; Apoderinae; Apoderus. REFERENCE 1 (bases 1 to 108) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Apoderus coryli whole genome shotgun (WGS) project has the project accession CAJVRQ000000000. This version of the project (01) has the accession number CAJVRQ010000000, and consists of sequences CAJVRQ010000001-CAJVRQ010000108. The assembly icApoCory1.1 is based on 59x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..108 /organism="Apoderus coryli" /mol_type="genomic DNA" /db_xref="taxon:201766" WGS CAJVRQ010000001-CAJVRQ010000108 // LOCUS CAJVRX010000000 5 rc DNA linear INV 28-JUL-2021 DEFINITION Pammene fasciana, whole genome shotgun sequencing project. ACCESSION CAJVRX000000000 VERSION CAJVRX000000000.1 DBLINK BioProject: PRJEB46632 BioSample: SAMEA7701530 KEYWORDS WGS. SOURCE Pammene fasciana ORGANISM Pammene fasciana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Grapholitini; Pammene. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pammene fasciana whole genome shotgun (WGS) project has the project accession CAJVRX000000000. This version of the project (01) has the accession number CAJVRX010000000, and consists of sequences CAJVRX010000001-CAJVRX010000005. The assembly ilPamFasc1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Pammene fasciana" /mol_type="genomic DNA" /db_xref="taxon:1101027" WGS CAJVRX010000001-CAJVRX010000005 // LOCUS CAJVRY010000000 8 rc DNA linear INV 28-JUL-2021 DEFINITION Pterostichus madidus, whole genome shotgun sequencing project. ACCESSION CAJVRY000000000 VERSION CAJVRY000000000.1 DBLINK BioProject: PRJEB46627 BioSample: SAMEA7520318 KEYWORDS WGS. SOURCE Pterostichus madidus ORGANISM Pterostichus madidus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Caraboidea; Carabidae; Harpalinae; Pterostichini; Pterostichus; Steropus. REFERENCE 1 (bases 1 to 8) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pterostichus madidus whole genome shotgun (WGS) project has the project accession CAJVRY000000000. This version of the project (01) has the accession number CAJVRY010000000, and consists of sequences CAJVRY010000001-CAJVRY010000008. The assembly icPteMadi1.1 is based on 34x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Some regions of the genome have large repeats with less certain structure than the rest of the assembly, most notably chromosomes 14,15 and 18. Chromosome 14 from 23.8mb onwards has strong Hi-C association with chromosome 18. FEATURES Location/Qualifiers source 1..8 /organism="Pterostichus madidus" /mol_type="genomic DNA" /db_xref="taxon:767470" WGS CAJVRY010000001-CAJVRY010000008 // LOCUS CAJVRP010000000 5 rc DNA linear INV 28-JUL-2021 DEFINITION Peribatodes rhomboidaria, whole genome shotgun sequencing project. ACCESSION CAJVRP000000000 VERSION CAJVRP000000000.1 DBLINK BioProject: PRJEB46633 BioSample: SAMEA7701524 KEYWORDS WGS. SOURCE Peribatodes rhomboidaria (willow beauty) ORGANISM Peribatodes rhomboidaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Peribatodes. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Peribatodes rhomboidaria whole genome shotgun (WGS) project has the project accession CAJVRP000000000. This version of the project (01) has the accession number CAJVRP010000000, and consists of sequences CAJVRP010000001-CAJVRP010000005. The assembly ilPerRhom1.1 is based on 44x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Peribatodes rhomboidaria" /mol_type="genomic DNA" /db_xref="taxon:190356" WGS CAJVRP010000001-CAJVRP010000005 // LOCUS CAJVRU010000000 3 rc DNA linear INV 28-JUL-2021 DEFINITION Furcula furcula, whole genome shotgun sequencing project. ACCESSION CAJVRU000000000 VERSION CAJVRU000000000.1 DBLINK BioProject: PRJEB46630 BioSample: SAMEA7746637 KEYWORDS WGS. SOURCE Furcula furcula ORGANISM Furcula furcula Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Stauropinae; Furcula. REFERENCE 1 (bases 1 to 3) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Furcula furcula whole genome shotgun (WGS) project has the project accession CAJVRU000000000. This version of the project (01) has the accession number CAJVRU010000000, and consists of sequences CAJVRU010000001-CAJVRU010000003. The assembly ilFurFurc1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3 /organism="Furcula furcula" /mol_type="genomic DNA" /db_xref="taxon:987943" WGS CAJVRU010000001-CAJVRU010000003 // LOCUS APVN02000000 46619 rc DNA linear INV 27-JUL-2021 DEFINITION Ladona fulva isolate sampled in the wild, whole genome shotgun sequencing project. ACCESSION APVN00000000 VERSION APVN00000000.2 DBLINK BioProject: PRJNA194433 BioSample: SAMN02178325 KEYWORDS WGS. SOURCE Ladona fulva (scarce chaser) ORGANISM Ladona fulva Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Palaeoptera; Odonata; Epiprocta; Anisoptera; Libellulidae; Ladona. REFERENCE 1 (bases 1 to 46619) AUTHORS Murali,S., Richards,S., Bandaranaike,D., Bellair,M., Blankenburg,K., Chao,H., Dinh,H., Doddapaneni,H., Dugan-Rocha,S., Elkadiri,S., Gnanaolivu,R., Hernandez,B., Skinner,E., Javaid,M., Lee,S., Li,M., Ming,W., Munidasa,M., Muniz,J., Nguyen,L., Hughes,D., Osuji,N., Pu,L.-L., Puazo,M., Qu,C., Quiroz,J., Raj,R., Weissenberger,G., Xin,Y., Zou,X., Han,Y., Worley,K., Muzny,D. and Gibbs,R. TITLE Ladona fulva Genome sequencing and assembly JOURNAL Unpublished REFERENCE 2 (bases 1 to 46619) AUTHORS Qu,J., Murali,S.C., Bandaranaike,D., Bellair,M., Blankenburg,K., Chao,H., Dinh,H., Doddapaneni,H., Downs,B., Dugan-Rocha,S., Elkadiri,S., Gnanaolivu,R.D., Hernandez,B., Javaid,M., Jayaseelan,J.C., Lee,S., Li,M., Ming,W., Munidasa,M., Muniz,J., Nguyen,L., Ongeri,F., Osuji,N., Pu,L.-L., Puazo,M., Qu,C., Quiroz,J., Raj,R., Weissenberger,G., Xin,Y., Zou,X., Han,Y., Richards,S., Worley,K., Muzny,D. and Gibbs,R. TITLE Direct Submission JOURNAL Submitted (01-APR-2013) Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA REFERENCE 3 (bases 1 to 46619) AUTHORS Murali,S., Richards,S., Bandaranaike,D., Bellair,M., Blankenburg,K., Chao,H., Dinh,H., Doddapaneni,H., Dugan-Rocha,S., Elkadiri,S., Gnanaolivu,R., Hughes,D., Lee,S., Li,M., Ming,W., Munidasa,M., Muniz,J., Nguyen,L., Osuji,N., Pu,L.-L., Puazo,M., Skinner,E., Qu,C., Quiroz,J., Raj,R., Weissenberger,G., Xin,Y., Zou,X., Han,Y., Worley,K., Muzny,D. and Gibbs,R. TITLE Direct Submission JOURNAL Submitted (26-OCT-2017) Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA REFERENCE 4 (bases 1 to 46619) AUTHORS Provataris,P., Ahn,S.-J., Jones,J., Niehuis,O., Robertson,H.M., Southgate,A., Poelchau,M.F., Hughes,D.S.T. and Richards,S. TITLE Direct Submission JOURNAL Submitted (19-JAN-2021) National Agricultural Library, USDA-ARS, 2150 Centre Ave, Fort Collins, CO 80526, USA REMARK ? COMMENT On Oct 31, 2017 this sequence version replaced APVN00000000.1. The Ladona fulva whole genome shotgun (WGS) project has the project accession APVN00000000. This version of the project (02) has the accession number APVN02000000, and consists of sequences APVN02000001-APVN02046619. Annotation was added to the contigs and scaffolds on July 2021. ##Genome-Assembly-Data-START## Assembly Date :: APR-2016 Assembly Method :: AllPaths v. 35218; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2; redundans v. 0.12c Assembly Name :: Lful_2.0 Expected Final Version :: no Genome Coverage :: 131.2x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..46619 /organism="Ladona fulva" /mol_type="genomic DNA" /isolate="sampled in the wild" /db_xref="taxon:123851" /sex="male" /country="Germany: Rhineland-Palatinate" /collection_date="07-May-2011" WGS APVN02000001-APVN02046619 WGS_SCAFLD KZ308113-KZ312454 // LOCUS CAJVQL010000000 716 rc DNA linear INV 21-JUL-2021 DEFINITION Thymelicus sylvestris, whole genome shotgun sequencing project. ACCESSION CAJVQL000000000 VERSION CAJVQL000000000.1 DBLINK BioProject: PRJEB46434 BioSample: SAMEA7523279 KEYWORDS WGS. SOURCE Thymelicus sylvestris (small skipper) ORGANISM Thymelicus sylvestris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Thymelicus. REFERENCE 1 (bases 1 to 716) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thymelicus sylvestris whole genome shotgun (WGS) project has the project accession CAJVQL000000000. This version of the project (01) has the accession number CAJVQL010000000, and consists of sequences CAJVQL010000001-CAJVQL010000716. The assembly ilThySylv1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..716 /organism="Thymelicus sylvestris" /mol_type="genomic DNA" /db_xref="taxon:272628" WGS CAJVQL010000001-CAJVQL010000716 // LOCUS CAJVQJ010000000 136 rc DNA linear INV 21-JUL-2021 DEFINITION Dolichovespula media, whole genome shotgun sequencing project. ACCESSION CAJVQJ000000000 VERSION CAJVQJ000000000.1 DBLINK BioProject: PRJEB46435 BioSample: SAMEA7520488 KEYWORDS WGS. SOURCE Dolichovespula media (median wasp) ORGANISM Dolichovespula media Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Dolichovespula. REFERENCE 1 (bases 1 to 136) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dolichovespula media whole genome shotgun (WGS) project has the project accession CAJVQJ000000000. This version of the project (01) has the accession number CAJVQJ010000000, and consists of sequences CAJVQJ010000001-CAJVQJ010000136. The assembly iyDolMedi1.1 is based on 74x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..136 /organism="Dolichovespula media" /mol_type="genomic DNA" /db_xref="taxon:881891" WGS CAJVQJ010000001-CAJVQJ010000136 // LOCUS CAJVRE010000000 115 rc DNA linear INV 22-JUL-2021 DEFINITION Bombus sylvestris, whole genome shotgun sequencing project. ACCESSION CAJVRE000000000 VERSION CAJVRE000000000.1 DBLINK BioProject: PRJEB46443 BioSample: SAMEA7520657 KEYWORDS WGS. SOURCE Bombus sylvestris (Psithyrus sylvestris) ORGANISM Bombus sylvestris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Bombus; Psithyrus. REFERENCE 1 (bases 1 to 115) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (20-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bombus sylvestris whole genome shotgun (WGS) project has the project accession CAJVRE000000000. This version of the project (01) has the accession number CAJVRE010000000, and consists of sequences CAJVRE010000001-CAJVRE010000115. The assembly iyBomSyle1.1 is based on 79x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..115 /organism="Bombus sylvestris" /mol_type="genomic DNA" /db_xref="taxon:30201" WGS CAJVRE010000001-CAJVRE010000115 // LOCUS CAJVQN010000000 2373 rc DNA linear INV 21-JUL-2021 DEFINITION Aelia acuminata, whole genome shotgun sequencing project. ACCESSION CAJVQN000000000 VERSION CAJVQN000000000.1 DBLINK BioProject: PRJEB46427 BioSample: SAMEA7520338 KEYWORDS WGS. SOURCE Aelia acuminata ORGANISM Aelia acuminata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Heteroptera; Panheteroptera; Pentatomomorpha; Pentatomoidea; Pentatomidae; Pentatominae; Aelia. REFERENCE 1 (bases 1 to 2373) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Aelia acuminata whole genome shotgun (WGS) project has the project accession CAJVQN000000000. This version of the project (01) has the accession number CAJVQN010000000, and consists of sequences CAJVQN010000001-CAJVQN010002373. The assembly ihAelAcum1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2373 /organism="Aelia acuminata" /mol_type="genomic DNA" /db_xref="taxon:1511221" WGS CAJVQN010000001-CAJVQN010002373 // LOCUS CAJVQV010000000 1551 rc DNA linear INV 21-JUL-2021 DEFINITION Chrysotoxum bicinctum, whole genome shotgun sequencing project. ACCESSION CAJVQV000000000 VERSION CAJVQV000000000.1 DBLINK BioProject: PRJEB46424 BioSample: SAMEA7520032 KEYWORDS WGS. SOURCE Chrysotoxum bicinctum ORGANISM Chrysotoxum bicinctum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Syrphini; Chrysotoxum. REFERENCE 1 (bases 1 to 1551) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysotoxum bicinctum whole genome shotgun (WGS) project has the project accession CAJVQV000000000. This version of the project (01) has the accession number CAJVQV010000000, and consists of sequences CAJVQV010000001-CAJVQV010001551. The assembly idChrBici1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1551 /organism="Chrysotoxum bicinctum" /mol_type="genomic DNA" /db_xref="taxon:323313" WGS CAJVQV010000001-CAJVQV010001551 // LOCUS CAJVQM010000000 42 rc DNA linear INV 21-JUL-2021 DEFINITION Pyrgus malvae, whole genome shotgun sequencing project. ACCESSION CAJVQM000000000 VERSION CAJVQM000000000.1 DBLINK BioProject: PRJEB46431 BioSample: SAMEA7523277 KEYWORDS WGS. SOURCE Pyrgus malvae (grizzled skipper) ORGANISM Pyrgus malvae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Pyrginae; Pyrgus. REFERENCE 1 (bases 1 to 42) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pyrgus malvae whole genome shotgun (WGS) project has the project accession CAJVQM000000000. This version of the project (01) has the accession number CAJVQM010000000, and consists of sequences CAJVQM010000001-CAJVQM010000042. The assembly ilPyrMalv3.1 is based on 69x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..42 /organism="Pyrgus malvae" /mol_type="genomic DNA" /db_xref="taxon:218760" WGS CAJVQM010000001-CAJVQM010000042 // LOCUS CAJVQP010000000 527 rc DNA linear INV 21-JUL-2021 DEFINITION Apamea monoglypha, whole genome shotgun sequencing project. ACCESSION CAJVQP000000000 VERSION CAJVQP000000000.1 DBLINK BioProject: PRJEB46429 BioSample: SAMEA7701555 KEYWORDS WGS. SOURCE Apamea monoglypha ORGANISM Apamea monoglypha Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Apameini; Apamea. REFERENCE 1 (bases 1 to 527) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Apamea monoglypha whole genome shotgun (WGS) project has the project accession CAJVQP000000000. This version of the project (01) has the accession number CAJVQP010000000, and consists of sequences CAJVQP010000001-CAJVQP010000527. The assembly ilApaMono1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..527 /organism="Apamea monoglypha" /mol_type="genomic DNA" /db_xref="taxon:875885" WGS CAJVQP010000001-CAJVQP010000527 // LOCUS CAJVQQ010000000 792 rc DNA linear INV 21-JUL-2021 DEFINITION Cantharis rustica, whole genome shotgun sequencing project. ACCESSION CAJVQQ000000000 VERSION CAJVQQ000000000.1 DBLINK BioProject: PRJEB46422 BioSample: SAMEA7524272 KEYWORDS WGS. SOURCE Cantharis rustica ORGANISM Cantharis rustica Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Elateroidea; Cantharidae; Cantharinae; Cantharis. REFERENCE 1 (bases 1 to 792) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cantharis rustica whole genome shotgun (WGS) project has the project accession CAJVQQ000000000. This version of the project (01) has the accession number CAJVQQ010000000, and consists of sequences CAJVQQ010000001-CAJVQQ010000792. The assembly icCanRust1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 contains a large heterochromatic region of low confidence at approximately 20-46Mb. This block consists of a number of scaffolds with high repeat content that can be localised to chromosome 2 but their order and orientation with respect to each other is unsure. Large islands of similar tandem repeat with high GC content are observed near both poles of Chromosome 1. Small islands of a related repeat are observed in all other chromosomes. FEATURES Location/Qualifiers source 1..792 /organism="Cantharis rustica" /mol_type="genomic DNA" /db_xref="taxon:195172" WGS CAJVQQ010000001-CAJVQQ010000792 // LOCUS CAJVQK010000000 948 rc DNA linear INV 21-JUL-2021 DEFINITION Dolichovespula media, whole genome shotgun sequencing project. ACCESSION CAJVQK000000000 VERSION CAJVQK000000000.1 DBLINK BioProject: PRJEB46436 BioSample: SAMEA7520488 KEYWORDS WGS. SOURCE Dolichovespula media (median wasp) ORGANISM Dolichovespula media Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Dolichovespula. REFERENCE 1 (bases 1 to 948) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dolichovespula media whole genome shotgun (WGS) project has the project accession CAJVQK000000000. This version of the project (01) has the accession number CAJVQK010000000, and consists of sequences CAJVQK010000001-CAJVQK010000948. The assembly iyDolMedi1.1 is based on 74x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..948 /organism="Dolichovespula media" /mol_type="genomic DNA" /db_xref="taxon:881891" WGS CAJVQK010000001-CAJVQK010000948 // LOCUS CAJVQY010000000 40 rc DNA linear INV 21-JUL-2021 DEFINITION Bombus hypnorum, whole genome shotgun sequencing project. ACCESSION CAJVQY000000000 VERSION CAJVQY000000000.1 DBLINK BioProject: PRJEB46442 BioSample: SAMEA7520655 KEYWORDS WGS. SOURCE Bombus hypnorum ORGANISM Bombus hypnorum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Bombus; Pyrobombus. REFERENCE 1 (bases 1 to 40) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bombus hypnorum whole genome shotgun (WGS) project has the project accession CAJVQY000000000. This version of the project (01) has the accession number CAJVQY010000000, and consists of sequences CAJVQY010000001-CAJVQY010000040. The assembly iyBomHypn1.1 is based on 33x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..40 /organism="Bombus hypnorum" /mol_type="genomic DNA" /db_xref="taxon:30191" WGS CAJVQY010000001-CAJVQY010000040 // LOCUS CAJVQU010000000 73 rc DNA linear INV 21-JUL-2021 DEFINITION Aelia acuminata, whole genome shotgun sequencing project. ACCESSION CAJVQU000000000 VERSION CAJVQU000000000.1 DBLINK BioProject: PRJEB46426 BioSample: SAMEA7520338 KEYWORDS WGS. SOURCE Aelia acuminata ORGANISM Aelia acuminata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Heteroptera; Panheteroptera; Pentatomomorpha; Pentatomoidea; Pentatomidae; Pentatominae; Aelia. REFERENCE 1 (bases 1 to 73) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Aelia acuminata whole genome shotgun (WGS) project has the project accession CAJVQU000000000. This version of the project (01) has the accession number CAJVQU010000000, and consists of sequences CAJVQU010000001-CAJVQU010000073. The assembly ihAelAcum1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..73 /organism="Aelia acuminata" /mol_type="genomic DNA" /db_xref="taxon:1511221" WGS CAJVQU010000001-CAJVQU010000073 // LOCUS CAJVQX010000000 86 rc DNA linear INV 21-JUL-2021 DEFINITION Dolichovespula saxonica, whole genome shotgun sequencing project. ACCESSION CAJVQX000000000 VERSION CAJVQX000000000.1 DBLINK BioProject: PRJEB46444 BioSample: SAMEA7520489 KEYWORDS WGS. SOURCE Dolichovespula saxonica ORGANISM Dolichovespula saxonica Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Dolichovespula. REFERENCE 1 (bases 1 to 86) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Dolichovespula saxonica whole genome shotgun (WGS) project has the project accession CAJVQX000000000. This version of the project (01) has the accession number CAJVQX010000000, and consists of sequences CAJVQX010000001-CAJVQX010000086. The assembly iyDolSaxo1.1 is based on 27x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..86 /organism="Dolichovespula saxonica" /mol_type="genomic DNA" /db_xref="taxon:85443" WGS CAJVQX010000001-CAJVQX010000086 // LOCUS CAJVQW010000000 87 rc DNA linear INV 21-JUL-2021 DEFINITION Chrysotoxum bicinctum, whole genome shotgun sequencing project. ACCESSION CAJVQW000000000 VERSION CAJVQW000000000.1 DBLINK BioProject: PRJEB46425 BioSample: SAMEA7520032 KEYWORDS WGS. SOURCE Chrysotoxum bicinctum ORGANISM Chrysotoxum bicinctum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Syrphini; Chrysotoxum. REFERENCE 1 (bases 1 to 87) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysotoxum bicinctum whole genome shotgun (WGS) project has the project accession CAJVQW000000000. This version of the project (01) has the accession number CAJVQW010000000, and consists of sequences CAJVQW010000001-CAJVQW010000087. The assembly idChrBici1.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..87 /organism="Chrysotoxum bicinctum" /mol_type="genomic DNA" /db_xref="taxon:323313" WGS CAJVQW010000001-CAJVQW010000087 // LOCUS CAJVQO010000000 10 rc DNA linear INV 21-JUL-2021 DEFINITION Cantharis rustica, whole genome shotgun sequencing project. ACCESSION CAJVQO000000000 VERSION CAJVQO000000000.1 DBLINK BioProject: PRJEB46423 BioSample: SAMEA7524272 KEYWORDS WGS. SOURCE Cantharis rustica ORGANISM Cantharis rustica Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Elateroidea; Cantharidae; Cantharinae; Cantharis. REFERENCE 1 (bases 1 to 10) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cantharis rustica whole genome shotgun (WGS) project has the project accession CAJVQO000000000. This version of the project (01) has the accession number CAJVQO010000000, and consists of sequences CAJVQO010000001-CAJVQO010000010. The assembly icCanRust1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 2 contains a large heterochromatic region of low confidence at approximately 20-46Mb. This block consists of a number of scaffolds with high repeat content that can be localised to chromosome 2 but their order and orientation with respect to each other is unsure. Large islands of similar tandem repeat with high GC content are observed near both poles of Chromosome 1. Small islands of a related repeat are observed in all other chromosomes. FEATURES Location/Qualifiers source 1..10 /organism="Cantharis rustica" /mol_type="genomic DNA" /db_xref="taxon:195172" WGS CAJVQO010000001-CAJVQO010000010 // LOCUS CAJVQS010000000 16 rc DNA linear INV 21-JUL-2021 DEFINITION Apamea monoglypha, whole genome shotgun sequencing project. ACCESSION CAJVQS000000000 VERSION CAJVQS000000000.1 DBLINK BioProject: PRJEB46430 BioSample: SAMEA7701555 KEYWORDS WGS. SOURCE Apamea monoglypha ORGANISM Apamea monoglypha Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Apameini; Apamea. REFERENCE 1 (bases 1 to 16) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Apamea monoglypha whole genome shotgun (WGS) project has the project accession CAJVQS000000000. This version of the project (01) has the accession number CAJVQS010000000, and consists of sequences CAJVQS010000001-CAJVQS010000016. The assembly ilApaMono1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..16 /organism="Apamea monoglypha" /mol_type="genomic DNA" /db_xref="taxon:875885" WGS CAJVQS010000001-CAJVQS010000016 // LOCUS CAJVQT010000000 5 rc DNA linear INV 21-JUL-2021 DEFINITION Pyrgus malvae, whole genome shotgun sequencing project. ACCESSION CAJVQT000000000 VERSION CAJVQT000000000.1 DBLINK BioProject: PRJEB46432 BioSample: SAMEA7523277 KEYWORDS WGS. SOURCE Pyrgus malvae (grizzled skipper) ORGANISM Pyrgus malvae Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Pyrginae; Pyrgus. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pyrgus malvae whole genome shotgun (WGS) project has the project accession CAJVQT000000000. This version of the project (01) has the accession number CAJVQT010000000, and consists of sequences CAJVQT010000001-CAJVQT010000005. The assembly ilPyrMalv3.1 is based on 69x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Pyrgus malvae" /mol_type="genomic DNA" /db_xref="taxon:218760" WGS CAJVQT010000001-CAJVQT010000005 // LOCUS CAJVQR010000000 4 rc DNA linear INV 21-JUL-2021 DEFINITION Thymelicus sylvestris, whole genome shotgun sequencing project. ACCESSION CAJVQR000000000 VERSION CAJVQR000000000.1 DBLINK BioProject: PRJEB46433 BioSample: SAMEA7523279 KEYWORDS WGS. SOURCE Thymelicus sylvestris (small skipper) ORGANISM Thymelicus sylvestris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Thymelicus. REFERENCE 1 (bases 1 to 4) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (19-JUL-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Thymelicus sylvestris whole genome shotgun (WGS) project has the project accession CAJVQR000000000. This version of the project (01) has the accession number CAJVQR010000000, and consists of sequences CAJVQR010000001-CAJVQR010000004. The assembly ilThySylv1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4 /organism="Thymelicus sylvestris" /mol_type="genomic DNA" /db_xref="taxon:272628" WGS CAJVQR010000001-CAJVQR010000004 // LOCUS JADCQN020000000 6737 rc DNA linear VRT 15-JUL-2021 DEFINITION Chelonia mydas isolate rCheMyd1, whole genome shotgun sequencing project. ACCESSION JADCQN000000000 VERSION JADCQN000000000.2 DBLINK BioProject: PRJNA561942 BioSample: SAMN12612360 KEYWORDS WGS. SOURCE Chelonia mydas (Green sea turtle) ORGANISM Chelonia mydas Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Americhelydia; Chelonioidea; Cheloniidae; Chelonia. REFERENCE 1 (bases 1 to 6737) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G., Tracey,A. and Jarvis,E.D. TITLE Chelonia mydas (Green sea turtle) genome, rCheMyd1, alternate haplotype, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 6737) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-OCT-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 6737) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G., Tracey,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (28-JUN-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Jul 15, 2021 this sequence version replaced JADCQN000000000.1. The Chelonia mydas whole genome shotgun (WGS) project has the project accession JADCQN000000000. This version of the project (02) has the accession number JADCQN020000000, and consists of sequences JADCQN020000001-JADCQN020006737. ##Genome-Assembly-Data-START## Assembly Date :: 28-MAY-2021 Assembly Method :: FALCON 1.3.0 v. 2018.31.08-03.06; FALCON-Unzip v. 1.2.0 6.0.0.47841; purge_dups v. github ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b; Scaff10x v. 4.1.0; Bionano Solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. SMRTLink7.0.1; Longranger Align v. 2.2.2; freebayes v. 1.3.1; gEVAL manual curation v. 2021-05-28; VGP assembly pipeline v. 1.6 Assembly Name :: rCheMyd1.alt.v2 Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..6737 /organism="Chelonia mydas" /mol_type="genomic DNA" /isolate="rCheMyd1" /db_xref="taxon:8469" /sex="male" /tissue_type="blood" /dev_stage="adult" /country="Israel: Mediterranean Sea" /lat_lon="31.814194 N 34.753376 E" /collection_date="2018-06-04" /collected_by="Yaron Tikochinski" WGS JADCQN020000001-JADCQN020006737 // LOCUS JADCQM020000000 92 rc DNA linear VRT 15-JUL-2021 DEFINITION Chelonia mydas isolate rCheMyd1, whole genome shotgun sequencing project. ACCESSION JADCQM000000000 VERSION JADCQM000000000.2 DBLINK BioProject: PRJNA561941 BioSample: SAMN12612360 KEYWORDS WGS. SOURCE Chelonia mydas (Green sea turtle) ORGANISM Chelonia mydas Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Americhelydia; Chelonioidea; Cheloniidae; Chelonia. REFERENCE 1 (bases 1 to 92) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G., Tracey,A. and Jarvis,E.D. TITLE Chelonia mydas (Green sea turtle) genome, rCheMyd1, primary haplotype, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 92) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-OCT-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 92) AUTHORS Mazzoni,C., Carrasco-Valenzuela,T., Uliano-Silva,M., Winkler,S., Formenti,G., Mountcastle,J., Haase,B., Pelan,S., Sims,Y., Tikochinski,Y., Howe,K., Fedrigo,O., Myers,G., Tracey,A. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (28-JUN-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Jul 14, 2021 this sequence version replaced JADCQM000000000.1. The Chelonia mydas whole genome shotgun (WGS) project has the project accession JADCQM000000000. This version of the project (02) has the accession number JADCQM020000000, and consists of sequences JADCQM020000001-JADCQM020000092. ##Genome-Assembly-Data-START## Assembly Date :: 28-MAY-2021 Assembly Method :: FALCON 1.3.0 v. 2018.31.08-03.06; FALCON-Unzip v. 1.2.0 6.0.0.47841; purge_dups v. github ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b; Scaff10x v. 4.1.0; Bionano Solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. SMRTLink7.0.1; Longranger Align v. 2.2.2; freebayes v. 1.3.1; gEVAL manual curation v. 2021-05-28; VGP assembly pipeline v. 1.6 Assembly Name :: rCheMyd1.pri.v2 Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..92 /organism="Chelonia mydas" /mol_type="genomic DNA" /isolate="rCheMyd1" /db_xref="taxon:8469" /sex="male" /tissue_type="blood" /dev_stage="adult" /country="Israel: Mediterranean Sea" /lat_lon="31.814194 N 34.753376 E" /collection_date="2018-06-04" /collected_by="Yaron Tikochinski" WGS JADCQM020000001-JADCQM020000092 WGS_SCAFLD CM026898-CM026925 // LOCUS CAADHW020000000 17082 rc DNA linear VRT 06-JUL-2021 DEFINITION Erpetoichthys calabaricus, whole genome shotgun sequencing project. ACCESSION CAADHW000000000 VERSION CAADHW000000000.2 DBLINK BioProject: PRJEB31582 BioSample: SAMEA104026374 KEYWORDS WGS. SOURCE Erpetoichthys calabaricus (reedfish) ORGANISM Erpetoichthys calabaricus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Polypteriformes; Polypteridae; Erpetoichthys. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (06-MAR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 17082) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (30-JUN-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Jul 7, 2021 this sequence version replaced CAADHW000000000.1. The Erpetoichthys calabaricus whole genome shotgun (WGS) project has the project accession CAADHW000000000. This version of the project (02) has the accession number CAADHW020000000, and consists of sequences CAADHW020000001-CAADHW020017082. The assembly fErpCal1.3 is based on 58x PacBio data, 31x 10X Genomics Chromium data, and 35x Arima Hi-C data generated at the Wellcome Sanger Institute, as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Solve, Hi-C based scaffolding with SALSA2, Arrow polishing using Merfin, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The GC profile of chromosome 11 is very unusual when compared with the other chromosomes. FEATURES Location/Qualifiers source 1..17082 /organism="Erpetoichthys calabaricus" /mol_type="genomic DNA" /db_xref="taxon:27687" WGS CAADHW020000001-CAADHW020017082 // LOCUS CAJVBA010000000 4021 rc DNA linear MAM 06-JUL-2021 DEFINITION Cervus elaphus, whole genome shotgun sequencing project. ACCESSION CAJVBA000000000 VERSION CAJVBA000000000.1 DBLINK BioProject: PRJEB45837 BioSample: SAMEA7523520 KEYWORDS WGS. SOURCE Cervus elaphus (red deer) ORGANISM Cervus elaphus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Cervidae; Cervinae; Cervus. REFERENCE 1 (bases 1 to 4021) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cervus elaphus whole genome shotgun (WGS) project has the project accession CAJVBA000000000. This version of the project (01) has the accession number CAJVBA010000000, and consists of sequences CAJVBA010000001-CAJVBA010004021. The assembly mCerEla1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny based on Cervus elaphus (Red deer) GCA_002197005.1. FEATURES Location/Qualifiers source 1..4021 /organism="Cervus elaphus" /mol_type="genomic DNA" /db_xref="taxon:9860" WGS CAJVBA010000001-CAJVBA010004021 // LOCUS CAJVAZ010000000 7136 rc DNA linear INV 06-JUL-2021 DEFINITION Ocypus olens, whole genome shotgun sequencing project. ACCESSION CAJVAZ000000000 VERSION CAJVAZ000000000.1 DBLINK BioProject: PRJEB45834 BioSample: SAMEA7520211 KEYWORDS WGS. SOURCE Ocypus olens ORGANISM Ocypus olens Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Staphyliniformia; Staphylinidae; Staphylininae group; Staphylininae; Staphylinini; Ocypus. REFERENCE 1 (bases 1 to 7136) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ocypus olens whole genome shotgun (WGS) project has the project accession CAJVAZ000000000. This version of the project (01) has the accession number CAJVAZ010000000, and consists of sequences CAJVAZ010000001-CAJVAZ010007136. The assembly icOcyOlen1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Order and orientation of scaffolds in the centromeric regions is less certain than in the rest of the assembly. FEATURES Location/Qualifiers source 1..7136 /organism="Ocypus olens" /mol_type="genomic DNA" /db_xref="taxon:662956" WGS CAJVAZ010000001-CAJVAZ010007136 // LOCUS CAJUUQ010000000 58 rc DNA linear INV 06-JUL-2021 DEFINITION Mythimna ferrago, whole genome shotgun sequencing project. ACCESSION CAJUUQ000000000 VERSION CAJUUQ000000000.1 DBLINK BioProject: PRJEB45326 BioSample: SAMEA7701536 KEYWORDS WGS. SOURCE Mythimna ferrago ORGANISM Mythimna ferrago Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Hadeninae; Mythimna. REFERENCE 1 (bases 1 to 58) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mythimna ferrago whole genome shotgun (WGS) project has the project accession CAJUUQ000000000. This version of the project (01) has the accession number CAJUUQ010000000, and consists of sequences CAJUUQ010000001-CAJUUQ010000058. The assembly ilMytFerr1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..58 /organism="Mythimna ferrago" /mol_type="genomic DNA" /db_xref="taxon:997540" WGS CAJUUQ010000001-CAJUUQ010000058 // LOCUS CAJVCN010000000 3263 rc DNA linear INV 06-JUL-2021 DEFINITION Xanthogramma pedissequum, whole genome shotgun sequencing project. ACCESSION CAJVCN000000000 VERSION CAJVCN000000000.1 DBLINK BioProject: PRJEB45688 BioSample: SAMEA7520951 KEYWORDS WGS. SOURCE Xanthogramma pedissequum ORGANISM Xanthogramma pedissequum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Syrphini; Xanthogramma. REFERENCE 1 (bases 1 to 3263) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Xanthogramma pedissequum whole genome shotgun (WGS) project has the project accession CAJVCN000000000. This version of the project (01) has the accession number CAJVCN010000000, and consists of sequences CAJVCN010000001-CAJVCN010003263. The assembly idXanPedi1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 1 contains a large, heterochromatic region of low confidence at approximately 113.44-242.17Mb. This block consists of numerous scaffolds with high repeat content that can be localised to chromosome 1 but their order and orientation is unsure. Hi-C data indicates that the region 32.39-38.38Mb on Chromosome X has a strong association with scaffolds labelled as Chromosome Y and Y_unloc. This highly repetitive region is likely misassembled containing data from both X and Y that was unable to be separated due to the limitations of current technologies. FEATURES Location/Qualifiers source 1..3263 /organism="Xanthogramma pedissequum" /mol_type="genomic DNA" /db_xref="taxon:414876" WGS CAJVCN010000001-CAJVCN010003263 // LOCUS CAJUZE010000000 915 rc DNA linear INV 06-JUL-2021 DEFINITION Ypsolopha scabrella, whole genome shotgun sequencing project. ACCESSION CAJUZE000000000 VERSION CAJUZE000000000.1 DBLINK BioProject: PRJEB45690 BioSample: SAMEA7701504 KEYWORDS WGS. SOURCE Ypsolopha scabrella ORGANISM Ypsolopha scabrella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Yponomeutoidea; Ypsolophidae; Ypsolopha. REFERENCE 1 (bases 1 to 915) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ypsolopha scabrella whole genome shotgun (WGS) project has the project accession CAJUZE000000000. This version of the project (01) has the accession number CAJUZE010000000, and consists of sequences CAJUZE010000001-CAJUZE010000915. The assembly ilYpsScab1.1 is based on 17x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..915 /organism="Ypsolopha scabrella" /mol_type="genomic DNA" /db_xref="taxon:1870435" WGS CAJUZE010000001-CAJUZE010000915 // LOCUS CAJUUP010000000 1778 rc DNA linear VRT 06-JUL-2021 DEFINITION Taurulus bubalis, whole genome shotgun sequencing project. ACCESSION CAJUUP000000000 VERSION CAJUUP000000000.1 DBLINK BioProject: PRJEB45316 BioSample: SAMEA7522994 KEYWORDS WGS. SOURCE Taurulus bubalis ORGANISM Taurulus bubalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Perciformes; Cottioidei; Cottales; Cottidae; Taurulus. REFERENCE 1 (bases 1 to 1778) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Taurulus bubalis whole genome shotgun (WGS) project has the project accession CAJUUP000000000. This version of the project (01) has the accession number CAJUUP010000000, and consists of sequences CAJUUP010000001-CAJUUP010001778. The assembly fTauBub2.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1778 /organism="Taurulus bubalis" /mol_type="genomic DNA" /db_xref="taxon:61643" WGS CAJUUP010000001-CAJUUP010001778 // LOCUS CAJUUJ010000000 433 rc DNA linear INV 06-JUL-2021 DEFINITION Tinea semifulvella, whole genome shotgun sequencing project. ACCESSION CAJUUJ000000000 VERSION CAJUUJ000000000.1 DBLINK BioProject: PRJEB45333 BioSample: SAMEA7520371 KEYWORDS WGS. SOURCE Tinea semifulvella ORGANISM Tinea semifulvella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tineoidea; Tineidae; Tineinae; Tinea. REFERENCE 1 (bases 1 to 433) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Tinea semifulvella whole genome shotgun (WGS) project has the project accession CAJUUJ000000000. This version of the project (01) has the accession number CAJUUJ010000000, and consists of sequences CAJUUJ010000001-CAJUUJ010000433. The assembly ilTinSemi1.1 is based on 45x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..433 /organism="Tinea semifulvella" /mol_type="genomic DNA" /db_xref="taxon:1101063" WGS CAJUUJ010000001-CAJUUJ010000433 // LOCUS CAJUUO010000000 400 rc DNA linear INV 06-JUL-2021 DEFINITION Chrysoteuchia culmella, whole genome shotgun sequencing project. ACCESSION CAJUUO000000000 VERSION CAJUUO000000000.1 DBLINK BioProject: PRJEB45322 BioSample: SAMEA7701502 KEYWORDS WGS. SOURCE Chrysoteuchia culmella ORGANISM Chrysoteuchia culmella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pyraloidea; Crambidae; Crambinae; Chrysoteuchia. REFERENCE 1 (bases 1 to 400) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysoteuchia culmella whole genome shotgun (WGS) project has the project accession CAJUUO000000000. This version of the project (01) has the accession number CAJUUO010000000, and consists of sequences CAJUUO010000001-CAJUUO010000400. The assembly ilChrCulm1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..400 /organism="Chrysoteuchia culmella" /mol_type="genomic DNA" /db_xref="taxon:1594250" WGS CAJUUO010000001-CAJUUO010000400 // LOCUS CAJVCF010000000 221 rc DNA linear INV 06-JUL-2021 DEFINITION Amphipyra berbera, whole genome shotgun sequencing project. ACCESSION CAJVCF000000000 VERSION CAJVCF000000000.1 DBLINK BioProject: PRJEB45916 BioSample: SAMEA7701493 KEYWORDS WGS. SOURCE Amphipyra berbera ORGANISM Amphipyra berbera Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Amphipyrinae; Amphipyra. REFERENCE 1 (bases 1 to 221) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Amphipyra berbera whole genome shotgun (WGS) project has the project accession CAJVCF000000000. This version of the project (01) has the accession number CAJVCF010000000, and consists of sequences CAJVCF010000001-CAJVCF010000221. The assembly ilAmpBerb1.1 is based on 41x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..221 /organism="Amphipyra berbera" /mol_type="genomic DNA" /db_xref="taxon:987877" WGS CAJVCF010000001-CAJVCF010000221 // LOCUS CAJUYA010000000 1130 rc DNA linear INV 06-JUL-2021 DEFINITION Cydia splendana, whole genome shotgun sequencing project. ACCESSION CAJUYA000000000 VERSION CAJUYA000000000.1 DBLINK BioProject: PRJEB45452 BioSample: SAMEA7701547 KEYWORDS WGS. SOURCE Cydia splendana ORGANISM Cydia splendana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Grapholitini; Cydia. REFERENCE 1 (bases 1 to 1130) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cydia splendana whole genome shotgun (WGS) project has the project accession CAJUYA000000000. This version of the project (01) has the accession number CAJUYA010000000, and consists of sequences CAJUYA010000001-CAJUYA010001130. The assembly ilCydSple1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1130 /organism="Cydia splendana" /mol_type="genomic DNA" /db_xref="taxon:1100963" WGS CAJUYA010000001-CAJUYA010001130 // LOCUS CAJUUN010000000 1475 rc DNA linear INV 06-JUL-2021 DEFINITION Malachius bipustulatus, whole genome shotgun sequencing project. ACCESSION CAJUUN000000000 VERSION CAJUUN000000000.1 DBLINK BioProject: PRJEB45314 BioSample: SAMEA7520537 KEYWORDS WGS. SOURCE Malachius bipustulatus ORGANISM Malachius bipustulatus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Melyridae; Malachiinae; Malachius. REFERENCE 1 (bases 1 to 1475) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malachius bipustulatus whole genome shotgun (WGS) project has the project accession CAJUUN000000000. This version of the project (01) has the accession number CAJUUN010000000, and consists of sequences CAJUUN010000001-CAJUUN010001475. The assembly icMalBipu1.1 is based on 32x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Due to ambiguous HiC signal and lack of additional evidence to support accurate placement several scaffolds that associate with Chromosome X by hic data have been submitted as unlocalised. These components are labelled SUPER_X_unloc_1-4. FEATURES Location/Qualifiers source 1..1475 /organism="Malachius bipustulatus" /mol_type="genomic DNA" /db_xref="taxon:295700" WGS CAJUUN010000001-CAJUUN010001475 // LOCUS CAJUUL010000000 839 rc DNA linear INV 06-JUL-2021 DEFINITION Noctua janthe, whole genome shotgun sequencing project. ACCESSION CAJUUL000000000 VERSION CAJUUL000000000.1 DBLINK BioProject: PRJEB45328 BioSample: SAMEA7701537 KEYWORDS WGS. SOURCE Noctua janthe ORGANISM Noctua janthe Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Noctua. REFERENCE 1 (bases 1 to 839) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Noctua janthe whole genome shotgun (WGS) project has the project accession CAJUUL000000000. This version of the project (01) has the accession number CAJUUL010000000, and consists of sequences CAJUUL010000001-CAJUUL010000839. The assembly ilNocJant1.1 is based on 48x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..839 /organism="Noctua janthe" /mol_type="genomic DNA" /db_xref="taxon:987995" WGS CAJUUL010000001-CAJUUL010000839 // LOCUS CAJUUT010000000 826 rc DNA linear INV 06-JUL-2021 DEFINITION Ennomos quercinarius, whole genome shotgun sequencing project. ACCESSION CAJUUT000000000 VERSION CAJUUT000000000.1 DBLINK BioProject: PRJEB45325 BioSample: SAMEA7701560 KEYWORDS WGS. SOURCE Ennomos quercinarius ORGANISM Ennomos quercinarius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Ennomos. REFERENCE 1 (bases 1 to 826) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ennomos quercinarius whole genome shotgun (WGS) project has the project accession CAJUUT000000000. This version of the project (01) has the accession number CAJUUT010000000, and consists of sequences CAJUUT010000001-CAJUUT010000826. The assembly ilEnnQuei1.1 is based on 47x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..826 /organism="Ennomos quercinarius" /mol_type="genomic DNA" /db_xref="taxon:875883" WGS CAJUUT010000001-CAJUUT010000826 // LOCUS CAJUXQ010000000 44 rc DNA linear INV 06-JUL-2021 DEFINITION Acronicta aceris, whole genome shotgun sequencing project. ACCESSION CAJUXQ000000000 VERSION CAJUXQ000000000.1 DBLINK BioProject: PRJEB45451 BioSample: SAMEA7701532 KEYWORDS WGS. SOURCE Acronicta aceris ORGANISM Acronicta aceris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Acronictinae; Acronicta. REFERENCE 1 (bases 1 to 44) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Acronicta aceris whole genome shotgun (WGS) project has the project accession CAJUXQ000000000. This version of the project (01) has the accession number CAJUXQ010000000, and consists of sequences CAJUXQ010000001-CAJUXQ010000044. The assembly ilAcrAcer1.1 is based on 39x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..44 /organism="Acronicta aceris" /mol_type="genomic DNA" /db_xref="taxon:987859" WGS CAJUXQ010000001-CAJUXQ010000044 // LOCUS CAJUUE010000000 430 rc DNA linear INV 06-JUL-2021 DEFINITION Parapoynx stratiotata, whole genome shotgun sequencing project. ACCESSION CAJUUE000000000 VERSION CAJUUE000000000.1 DBLINK BioProject: PRJEB45331 BioSample: SAMEA7519920 KEYWORDS WGS. SOURCE Parapoynx stratiotata ORGANISM Parapoynx stratiotata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pyraloidea; Crambidae; Nymphulinae; Parapoynx. REFERENCE 1 (bases 1 to 430) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Parapoynx stratiotata whole genome shotgun (WGS) project has the project accession CAJUUE000000000. This version of the project (01) has the accession number CAJUUE010000000, and consists of sequences CAJUUE010000001-CAJUUE010000430. The assembly ilParStra1.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..430 /organism="Parapoynx stratiotata" /mol_type="genomic DNA" /db_xref="taxon:1594321" WGS CAJUUE010000001-CAJUUE010000430 // LOCUS CAJUUI010000000 2494 rc DNA linear INV 06-JUL-2021 DEFINITION Bembecia ichneumoniformis, whole genome shotgun sequencing project. ACCESSION CAJUUI000000000 VERSION CAJUUI000000000.1 DBLINK BioProject: PRJEB45318 BioSample: SAMEA7701282 KEYWORDS WGS. SOURCE Bembecia ichneumoniformis (six-belted clearwing) ORGANISM Bembecia ichneumoniformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sesioidea; Sesiidae; Sesiinae; Synanthedonini; Bembecia. REFERENCE 1 (bases 1 to 2494) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bembecia ichneumoniformis whole genome shotgun (WGS) project has the project accession CAJUUI000000000. This version of the project (01) has the accession number CAJUUI010000000, and consists of sequences CAJUUI010000001-CAJUUI010002494. The assembly ilBemIchn1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2494 /organism="Bembecia ichneumoniformis" /mol_type="genomic DNA" /db_xref="taxon:301037" WGS CAJUUI010000001-CAJUUI010002494 // LOCUS CAJUUC010000000 57 rc DNA linear INV 06-JUL-2021 DEFINITION Carcina quercana, whole genome shotgun sequencing project. ACCESSION CAJUUC000000000 VERSION CAJUUC000000000.1 DBLINK BioProject: PRJEB45320 BioSample: SAMEA7519850 KEYWORDS WGS. SOURCE Carcina quercana ORGANISM Carcina quercana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Gelechioidea; Peleopodidae; Carcina. REFERENCE 1 (bases 1 to 57) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Carcina quercana whole genome shotgun (WGS) project has the project accession CAJUUC000000000. This version of the project (01) has the accession number CAJUUC010000000, and consists of sequences CAJUUC010000001-CAJUUC010000057. The assembly ilCarQuer1.1 is based on 57x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..57 /organism="Carcina quercana" /mol_type="genomic DNA" /db_xref="taxon:116121" WGS CAJUUC010000001-CAJUUC010000057 // LOCUS CAJUXO010000000 710 rc DNA linear INV 06-JUL-2021 DEFINITION Cerceris rybyensis, whole genome shotgun sequencing project. ACCESSION CAJUXO000000000 VERSION CAJUXO000000000.1 DBLINK BioProject: PRJEB45454 BioSample: SAMEA7701329 KEYWORDS WGS. SOURCE Cerceris rybyensis ORGANISM Cerceris rybyensis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Philanthinae; Cercerini; Cerceris. REFERENCE 1 (bases 1 to 710) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cerceris rybyensis whole genome shotgun (WGS) project has the project accession CAJUXO000000000. This version of the project (01) has the accession number CAJUXO010000000, and consists of sequences CAJUXO010000001-CAJUXO010000710. The assembly iyCerRyby1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..710 /organism="Cerceris rybyensis" /mol_type="genomic DNA" /db_xref="taxon:1167272" WGS CAJUXO010000001-CAJUXO010000710 // LOCUS CAJUZK010000000 452 rc DNA linear INV 06-JUL-2021 DEFINITION Lineus longissimus, whole genome shotgun sequencing project. ACCESSION CAJUZK000000000 VERSION CAJUZK000000000.1 DBLINK BioProject: PRJEB45697 BioSample: SAMEA7522833 KEYWORDS WGS. SOURCE Lineus longissimus ORGANISM Lineus longissimus Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Nemertea; Pilidiophora; Heteronemertea; Lineidae; Lineus. REFERENCE 1 (bases 1 to 452) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lineus longissimus whole genome shotgun (WGS) project has the project accession CAJUZK000000000. This version of the project (01) has the accession number CAJUZK010000000, and consists of sequences CAJUZK010000001-CAJUZK010000452. The assembly tnLinLong1.1 is based on 79x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 5 contains a large inversion between sister chromatids at approximately 11.1-15.4Mb. FEATURES Location/Qualifiers source 1..452 /organism="Lineus longissimus" /mol_type="genomic DNA" /db_xref="taxon:88925" WGS CAJUZK010000001-CAJUZK010000452 // LOCUS CAJUZC010000000 1048 rc DNA linear INV 06-JUL-2021 DEFINITION Adalia bipunctata, whole genome shotgun sequencing project. ACCESSION CAJUZC000000000 VERSION CAJUZC000000000.1 DBLINK BioProject: PRJEB45687 BioSample: SAMEA9089055 KEYWORDS WGS. SOURCE Adalia bipunctata (two-spotted ladybird beetle) ORGANISM Adalia bipunctata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Adalia. REFERENCE 1 (bases 1 to 1048) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Adalia bipunctata whole genome shotgun (WGS) project has the project accession CAJUZC000000000. This version of the project (01) has the accession number CAJUZC010000000, and consists of sequences CAJUZC010000001-CAJUZC010001048. The assembly icAdaBipu1.1 is based on 48x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1048 /organism="Adalia bipunctata" /mol_type="genomic DNA" /db_xref="taxon:7084" WGS CAJUZC010000001-CAJUZC010001048 // LOCUS CAJVCD010000000 325 rc DNA linear INV 06-JUL-2021 DEFINITION Bibio marci, whole genome shotgun sequencing project. ACCESSION CAJVCD000000000 VERSION CAJVCD000000000.1 DBLINK BioProject: PRJEB45914 BioSample: SAMEA7524263 KEYWORDS WGS. SOURCE Bibio marci (St. Mark's fly) ORGANISM Bibio marci Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Bibionoidea; Bibionidae; Bibio. REFERENCE 1 (bases 1 to 325) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bibio marci whole genome shotgun (WGS) project has the project accession CAJVCD000000000. This version of the project (01) has the accession number CAJVCD010000000, and consists of sequences CAJVCD010000001-CAJVCD010000325. The assembly idBibMarc1.1 is based on 53x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Unknown sex chromosome system, no Y found. X assembly has good contiguity and good HiC linking across scaffold gaps. FEATURES Location/Qualifiers source 1..325 /organism="Bibio marci" /mol_type="genomic DNA" /db_xref="taxon:189979" WGS CAJVCD010000001-CAJVCD010000325 // LOCUS CAJUXM010000000 920 rc DNA linear INV 06-JUL-2021 DEFINITION Nysson spinosus, whole genome shotgun sequencing project. ACCESSION CAJUXM000000000 VERSION CAJUXM000000000.1 DBLINK BioProject: PRJEB45458 BioSample: SAMEA7520702 KEYWORDS WGS. SOURCE Nysson spinosus ORGANISM Nysson spinosus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Bembicinae; Nyssonini; Nysson. REFERENCE 1 (bases 1 to 920) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Nysson spinosus whole genome shotgun (WGS) project has the project accession CAJUXM000000000. This version of the project (01) has the accession number CAJUXM010000000, and consists of sequences CAJUXM010000001-CAJUXM010000920. The assembly iyNysSpin1.1 is based on 54x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Some uncertainty over chromosome assignment. From Hi-C evidence it appears that the 26 euchromatic blocks represent 26 individual chromosomes with a large amount of heterochromatic sequence unplaceable. FEATURES Location/Qualifiers source 1..920 /organism="Nysson spinosus" /mol_type="genomic DNA" /db_xref="taxon:2495127" WGS CAJUXM010000001-CAJUXM010000920 // LOCUS CAJUYZ010000000 533 rc DNA linear INV 06-JUL-2021 DEFINITION Bombus terrestris, whole genome shotgun sequencing project. ACCESSION CAJUYZ000000000 VERSION CAJUYZ000000000.1 DBLINK BioProject: PRJEB45695 BioSample: SAMEA7520487 KEYWORDS WGS. SOURCE Bombus terrestris (buff-tailed bumblebee) ORGANISM Bombus terrestris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Bombus; Bombus. REFERENCE 1 (bases 1 to 533) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bombus terrestris whole genome shotgun (WGS) project has the project accession CAJUYZ000000000. This version of the project (01) has the accession number CAJUYZ010000000, and consists of sequences CAJUYZ010000001-CAJUYZ010000533. The assembly iyBomTerr1.1 is based on 57x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny based on Bombus terrestris (buff-tailed bumblebee) GCA_000214255.1. Many unplaced scaffolds are composed entirely of a 10mer repeat which we note occurs in other Bombus assemblies. FEATURES Location/Qualifiers source 1..533 /organism="Bombus terrestris" /mol_type="genomic DNA" /db_xref="taxon:30195" WGS CAJUYZ010000001-CAJUYZ010000533 // LOCUS CAJUZB010000000 985 rc DNA linear INV 06-JUL-2021 DEFINITION Andrena haemorrhoa, whole genome shotgun sequencing project. ACCESSION CAJUZB000000000 VERSION CAJUZB000000000.1 DBLINK BioProject: PRJEB45693 BioSample: SAMEA7520535 KEYWORDS WGS. SOURCE Andrena haemorrhoa ORGANISM Andrena haemorrhoa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Andrenidae; Andreninae; Andrena; Taeniandrena. REFERENCE 1 (bases 1 to 985) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Andrena haemorrhoa whole genome shotgun (WGS) project has the project accession CAJUZB000000000. This version of the project (01) has the accession number CAJUZB010000000, and consists of sequences CAJUZB010000001-CAJUZB010000985. The assembly iyAndHaem1.1 is based on 77x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..985 /organism="Andrena haemorrhoa" /mol_type="genomic DNA" /db_xref="taxon:444401" WGS CAJUZB010000001-CAJUZB010000985 // LOCUS CAJUXN010000000 543 rc DNA linear INV 06-JUL-2021 DEFINITION Ectemnius continuus, whole genome shotgun sequencing project. ACCESSION CAJUXN000000000 VERSION CAJUXN000000000.1 DBLINK BioProject: PRJEB45457 BioSample: SAMEA7520490 KEYWORDS WGS. SOURCE Ectemnius continuus ORGANISM Ectemnius continuus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Crabroninae; Crabronini; Crabronina; Ectemnius. REFERENCE 1 (bases 1 to 543) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ectemnius continuus whole genome shotgun (WGS) project has the project accession CAJUXN000000000. This version of the project (01) has the accession number CAJUXN010000000, and consists of sequences CAJUXN010000001-CAJUXN010000543. The assembly iyEctCont1.1 is based on 92x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..543 /organism="Ectemnius continuus" /mol_type="genomic DNA" /db_xref="taxon:1126389" WGS CAJUXN010000001-CAJUXN010000543 // LOCUS CAJUUS010000000 4397 rc DNA linear INV 06-JUL-2021 DEFINITION Vespa crabro, whole genome shotgun sequencing project. ACCESSION CAJUUS000000000 VERSION CAJUUS000000000.1 DBLINK BioProject: PRJEB45334 BioSample: SAMEA7520500 KEYWORDS WGS. SOURCE Vespa crabro (European hornet) ORGANISM Vespa crabro Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespa. REFERENCE 1 (bases 1 to 4397) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespa crabro whole genome shotgun (WGS) project has the project accession CAJUUS000000000. This version of the project (01) has the accession number CAJUUS010000000, and consists of sequences CAJUUS010000001-CAJUUS010004397. The assembly iyVesCrab1.1 is based on 70x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..4397 /organism="Vespa crabro" /mol_type="genomic DNA" /db_xref="taxon:7445" WGS CAJUUS010000001-CAJUUS010004397 // LOCUS CAJVBL010000000 110 rc DNA linear MAM 06-JUL-2021 DEFINITION Cervus elaphus, whole genome shotgun sequencing project. ACCESSION CAJVBL000000000 VERSION CAJVBL000000000.1 DBLINK BioProject: PRJEB45838 BioSample: SAMEA7523520 KEYWORDS WGS. SOURCE Cervus elaphus (red deer) ORGANISM Cervus elaphus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Cervidae; Cervinae; Cervus. REFERENCE 1 (bases 1 to 110) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cervus elaphus whole genome shotgun (WGS) project has the project accession CAJVBL000000000. This version of the project (01) has the accession number CAJVBL010000000, and consists of sequences CAJVBL010000001-CAJVBL010000110. The assembly mCerEla1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny based on Cervus elaphus (Red deer) GCA_002197005.1. FEATURES Location/Qualifiers source 1..110 /organism="Cervus elaphus" /mol_type="genomic DNA" /db_xref="taxon:9860" WGS CAJVBL010000001-CAJVBL010000110 // LOCUS CAJUYC010000000 132 rc DNA linear INV 06-JUL-2021 DEFINITION Nysson spinosus, whole genome shotgun sequencing project. ACCESSION CAJUYC000000000 VERSION CAJUYC000000000.1 DBLINK BioProject: PRJEB45459 BioSample: SAMEA7520702 KEYWORDS WGS. SOURCE Nysson spinosus ORGANISM Nysson spinosus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Bembicinae; Nyssonini; Nysson. REFERENCE 1 (bases 1 to 132) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Nysson spinosus whole genome shotgun (WGS) project has the project accession CAJUYC000000000. This version of the project (01) has the accession number CAJUYC010000000, and consists of sequences CAJUYC010000001-CAJUYC010000132. The assembly iyNysSpin1.1 is based on 54x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Some uncertainty over chromosome assignment. From Hi-C evidence it appears that the 26 euchromatic blocks represent 26 individual chromosomes with a large amount of heterochromatic sequence unplaceable. FEATURES Location/Qualifiers source 1..132 /organism="Nysson spinosus" /mol_type="genomic DNA" /db_xref="taxon:2495127" WGS CAJUYC010000001-CAJUYC010000132 // LOCUS CAJUYY010000000 237 rc DNA linear INV 06-JUL-2021 DEFINITION Bombus terrestris, whole genome shotgun sequencing project. ACCESSION CAJUYY000000000 VERSION CAJUYY000000000.1 DBLINK BioProject: PRJEB45694 BioSample: SAMEA7520487 KEYWORDS WGS. SOURCE Bombus terrestris (buff-tailed bumblebee) ORGANISM Bombus terrestris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Bombus; Bombus. REFERENCE 1 (bases 1 to 237) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bombus terrestris whole genome shotgun (WGS) project has the project accession CAJUYY000000000. This version of the project (01) has the accession number CAJUYY010000000, and consists of sequences CAJUYY010000001-CAJUYY010000237. The assembly iyBomTerr1.1 is based on 57x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny based on Bombus terrestris (buff-tailed bumblebee) GCA_000214255.1. Many unplaced scaffolds are composed entirely of a 10mer repeat which we note occurs in other Bombus assemblies. FEATURES Location/Qualifiers source 1..237 /organism="Bombus terrestris" /mol_type="genomic DNA" /db_xref="taxon:30195" WGS CAJUYY010000001-CAJUYY010000237 // LOCUS CAJUYE010000000 83 rc DNA linear INV 06-JUL-2021 DEFINITION Cydia splendana, whole genome shotgun sequencing project. ACCESSION CAJUYE000000000 VERSION CAJUYE000000000.1 DBLINK BioProject: PRJEB45453 BioSample: SAMEA7701547 KEYWORDS WGS. SOURCE Cydia splendana ORGANISM Cydia splendana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Olethreutinae; Grapholitini; Cydia. REFERENCE 1 (bases 1 to 83) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cydia splendana whole genome shotgun (WGS) project has the project accession CAJUYE000000000. This version of the project (01) has the accession number CAJUYE010000000, and consists of sequences CAJUYE010000001-CAJUYE010000083. The assembly ilCydSple1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..83 /organism="Cydia splendana" /mol_type="genomic DNA" /db_xref="taxon:1100963" WGS CAJUYE010000001-CAJUYE010000083 // LOCUS CAJUZA010000000 395 rc DNA linear INV 06-JUL-2021 DEFINITION Andrena haemorrhoa, whole genome shotgun sequencing project. ACCESSION CAJUZA000000000 VERSION CAJUZA000000000.1 DBLINK BioProject: PRJEB45692 BioSample: SAMEA7520535 KEYWORDS WGS. SOURCE Andrena haemorrhoa ORGANISM Andrena haemorrhoa Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Andrenidae; Andreninae; Andrena; Taeniandrena. REFERENCE 1 (bases 1 to 395) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Andrena haemorrhoa whole genome shotgun (WGS) project has the project accession CAJUZA000000000. This version of the project (01) has the accession number CAJUZA010000000, and consists of sequences CAJUZA010000001-CAJUZA010000395. The assembly iyAndHaem1.1 is based on 77x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..395 /organism="Andrena haemorrhoa" /mol_type="genomic DNA" /db_xref="taxon:444401" WGS CAJUZA010000001-CAJUZA010000395 // LOCUS CAJUXP010000000 657 rc DNA linear INV 06-JUL-2021 DEFINITION Cerceris rybyensis, whole genome shotgun sequencing project. ACCESSION CAJUXP000000000 VERSION CAJUXP000000000.1 DBLINK BioProject: PRJEB45455 BioSample: SAMEA7701329 KEYWORDS WGS. SOURCE Cerceris rybyensis ORGANISM Cerceris rybyensis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Philanthinae; Cercerini; Cerceris. REFERENCE 1 (bases 1 to 657) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Cerceris rybyensis whole genome shotgun (WGS) project has the project accession CAJUXP000000000. This version of the project (01) has the accession number CAJUXP010000000, and consists of sequences CAJUXP010000001-CAJUXP010000657. The assembly iyCerRyby1.1 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..657 /organism="Cerceris rybyensis" /mol_type="genomic DNA" /db_xref="taxon:1167272" WGS CAJUXP010000001-CAJUXP010000657 // LOCUS CAADRL030000000 150 rc DNA linear VRT 06-JUL-2021 DEFINITION Erpetoichthys calabaricus, whole genome shotgun sequencing project. ACCESSION CAADRL000000000 VERSION CAADRL000000000.3 DBLINK BioProject: PRJEB31579 BioSample: SAMEA104026374 KEYWORDS WGS. SOURCE Erpetoichthys calabaricus (reedfish) ORGANISM Erpetoichthys calabaricus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Polypteriformes; Polypteridae; Erpetoichthys. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-MAR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 150) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (30-JUN-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Jul 7, 2021 this sequence version replaced CAADRL000000000.2. The Erpetoichthys calabaricus whole genome shotgun (WGS) project has the project accession CAADRL000000000. This version of the project (03) has the accession number CAADRL030000000, and consists of sequences CAADRL030000001-CAADRL030000150. The assembly fErpCal1.3 is based on 58x PacBio data, 31x 10X Genomics Chromium data, and 35x Arima Hi-C data generated at the Wellcome Sanger Institute, as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Solve, Hi-C based scaffolding with SALSA2, Arrow polishing using Merfin, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. The GC profile of chromosome 11 is very unusual when compared with the other chromosomes. FEATURES Location/Qualifiers source 1..150 /organism="Erpetoichthys calabaricus" /mol_type="genomic DNA" /db_xref="taxon:27687" WGS CAADRL030000001-CAADRL030000150 // LOCUS CAJVCO010000000 478 rc DNA linear INV 06-JUL-2021 DEFINITION Xanthogramma pedissequum, whole genome shotgun sequencing project. ACCESSION CAJVCO000000000 VERSION CAJVCO000000000.1 DBLINK BioProject: PRJEB45689 BioSample: SAMEA7520951 KEYWORDS WGS. SOURCE Xanthogramma pedissequum ORGANISM Xanthogramma pedissequum Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Syrphinae; Syrphini; Xanthogramma. REFERENCE 1 (bases 1 to 478) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Xanthogramma pedissequum whole genome shotgun (WGS) project has the project accession CAJVCO000000000. This version of the project (01) has the accession number CAJVCO010000000, and consists of sequences CAJVCO010000001-CAJVCO010000478. The assembly idXanPedi1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 1 contains a large, heterochromatic region of low confidence at approximately 113.44-242.17Mb. This block consists of numerous scaffolds with high repeat content that can be localised to chromosome 1 but their order and orientation is unsure. Hi-C data indicates that the region 32.39-38.38Mb on Chromosome X has a strong association with scaffolds labelled as Chromosome Y and Y_unloc. This highly repetitive region is likely misassembled containing data from both X and Y that was unable to be separated due to the limitations of current technologies. FEATURES Location/Qualifiers source 1..478 /organism="Xanthogramma pedissequum" /mol_type="genomic DNA" /db_xref="taxon:414876" WGS CAJVCO010000001-CAJVCO010000478 // LOCUS CAJUYD010000000 333 rc DNA linear INV 06-JUL-2021 DEFINITION Ectemnius continuus, whole genome shotgun sequencing project. ACCESSION CAJUYD000000000 VERSION CAJUYD000000000.1 DBLINK BioProject: PRJEB45456 BioSample: SAMEA7520490 KEYWORDS WGS. SOURCE Ectemnius continuus ORGANISM Ectemnius continuus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Crabroninae; Crabronini; Crabronina; Ectemnius. REFERENCE 1 (bases 1 to 333) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (04-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ectemnius continuus whole genome shotgun (WGS) project has the project accession CAJUYD000000000. This version of the project (01) has the accession number CAJUYD010000000, and consists of sequences CAJUYD010000001-CAJUYD010000333. The assembly iyEctCont1.1 is based on 92x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..333 /organism="Ectemnius continuus" /mol_type="genomic DNA" /db_xref="taxon:1126389" WGS CAJUYD010000001-CAJUYD010000333 // LOCUS CAJUZD010000000 107 rc DNA linear INV 06-JUL-2021 DEFINITION Adalia bipunctata, whole genome shotgun sequencing project. ACCESSION CAJUZD000000000 VERSION CAJUZD000000000.1 DBLINK BioProject: PRJEB45686 BioSample: SAMEA9089055 KEYWORDS WGS. SOURCE Adalia bipunctata (two-spotted ladybird beetle) ORGANISM Adalia bipunctata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Adalia. REFERENCE 1 (bases 1 to 107) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Adalia bipunctata whole genome shotgun (WGS) project has the project accession CAJUZD000000000. This version of the project (01) has the accession number CAJUZD010000000, and consists of sequences CAJUZD010000001-CAJUZD010000107. The assembly icAdaBipu1.1 is based on 48x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..107 /organism="Adalia bipunctata" /mol_type="genomic DNA" /db_xref="taxon:7084" WGS CAJUZD010000001-CAJUZD010000107 // LOCUS CAJUUU010000000 14 rc DNA linear INV 06-JUL-2021 DEFINITION Mythimna ferrago, whole genome shotgun sequencing project. ACCESSION CAJUUU000000000 VERSION CAJUUU000000000.1 DBLINK BioProject: PRJEB45327 BioSample: SAMEA7701536 KEYWORDS WGS. SOURCE Mythimna ferrago ORGANISM Mythimna ferrago Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Hadeninae; Mythimna. REFERENCE 1 (bases 1 to 14) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Mythimna ferrago whole genome shotgun (WGS) project has the project accession CAJUUU000000000. This version of the project (01) has the accession number CAJUUU010000000, and consists of sequences CAJUUU010000001-CAJUUU010000014. The assembly ilMytFerr1.1 is based on 31x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..14 /organism="Mythimna ferrago" /mol_type="genomic DNA" /db_xref="taxon:997540" WGS CAJUUU010000001-CAJUUU010000014 // LOCUS CAJVAQ010000000 104 rc DNA linear INV 06-JUL-2021 DEFINITION Ectemnius lituratus, whole genome shotgun sequencing project. ACCESSION CAJVAQ000000000 VERSION CAJVAQ000000000.1 DBLINK BioProject: PRJEB45835 BioSample: SAMEA7520491 KEYWORDS WGS. SOURCE Ectemnius lituratus ORGANISM Ectemnius lituratus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Crabroninae; Crabronini; Crabronina; Ectemnius. REFERENCE 1 (bases 1 to 104) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ectemnius lituratus whole genome shotgun (WGS) project has the project accession CAJVAQ000000000. This version of the project (01) has the accession number CAJVAQ010000000, and consists of sequences CAJVAQ010000001-CAJVAQ010000104. The assembly iyEctLitu1.1 is based on 110x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..104 /organism="Ectemnius lituratus" /mol_type="genomic DNA" /db_xref="taxon:2495015" WGS CAJVAQ010000001-CAJVAQ010000104 // LOCUS CAJUUB010000000 80 rc DNA linear INV 06-JUL-2021 DEFINITION Vespa crabro, whole genome shotgun sequencing project. ACCESSION CAJUUB000000000 VERSION CAJUUB000000000.1 DBLINK BioProject: PRJEB45335 BioSample: SAMEA7520500 KEYWORDS WGS. SOURCE Vespa crabro (European hornet) ORGANISM Vespa crabro Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespa. REFERENCE 1 (bases 1 to 80) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespa crabro whole genome shotgun (WGS) project has the project accession CAJUUB000000000. This version of the project (01) has the accession number CAJUUB010000000, and consists of sequences CAJUUB010000001-CAJUUB010000080. The assembly iyVesCrab1.1 is based on 70x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..80 /organism="Vespa crabro" /mol_type="genomic DNA" /db_xref="taxon:7445" WGS CAJUUB010000001-CAJUUB010000080 // LOCUS CAJUUM010000000 41 rc DNA linear INV 06-JUL-2021 DEFINITION Malachius bipustulatus, whole genome shotgun sequencing project. ACCESSION CAJUUM000000000 VERSION CAJUUM000000000.1 DBLINK BioProject: PRJEB45315 BioSample: SAMEA7520537 KEYWORDS WGS. SOURCE Malachius bipustulatus ORGANISM Malachius bipustulatus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Melyridae; Malachiinae; Malachius. REFERENCE 1 (bases 1 to 41) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Malachius bipustulatus whole genome shotgun (WGS) project has the project accession CAJUUM000000000. This version of the project (01) has the accession number CAJUUM010000000, and consists of sequences CAJUUM010000001-CAJUUM010000041. The assembly icMalBipu1.1 is based on 32x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Due to ambiguous HiC signal and lack of additional evidence to support accurate placement several scaffolds that associate with Chromosome X by hic data have been submitted as unlocalised. These components are labelled SUPER_X_unloc_1-4. FEATURES Location/Qualifiers source 1..41 /organism="Malachius bipustulatus" /mol_type="genomic DNA" /db_xref="taxon:295700" WGS CAJUUM010000001-CAJUUM010000041 // LOCUS CAJVAY010000000 168 rc DNA linear INV 06-JUL-2021 DEFINITION Ocypus olens, whole genome shotgun sequencing project. ACCESSION CAJVAY000000000 VERSION CAJVAY000000000.1 DBLINK BioProject: PRJEB45833 BioSample: SAMEA7520211 KEYWORDS WGS. SOURCE Ocypus olens ORGANISM Ocypus olens Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Staphyliniformia; Staphylinidae; Staphylininae group; Staphylininae; Staphylinini; Ocypus. REFERENCE 1 (bases 1 to 168) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ocypus olens whole genome shotgun (WGS) project has the project accession CAJVAY000000000. This version of the project (01) has the accession number CAJVAY010000000, and consists of sequences CAJVAY010000001-CAJVAY010000168. The assembly icOcyOlen1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Order and orientation of scaffolds in the centromeric regions is less certain than in the rest of the assembly. FEATURES Location/Qualifiers source 1..168 /organism="Ocypus olens" /mol_type="genomic DNA" /db_xref="taxon:662956" WGS CAJVAY010000001-CAJVAY010000168 // LOCUS CAJVAM010000000 79 rc DNA linear INV 06-JUL-2021 DEFINITION Ectemnius lituratus, whole genome shotgun sequencing project. ACCESSION CAJVAM000000000 VERSION CAJVAM000000000.1 DBLINK BioProject: PRJEB45836 BioSample: SAMEA7520491 KEYWORDS WGS. SOURCE Ectemnius lituratus ORGANISM Ectemnius lituratus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Spheciformes; Crabronidae; Crabroninae; Crabronini; Crabronina; Ectemnius. REFERENCE 1 (bases 1 to 79) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ectemnius lituratus whole genome shotgun (WGS) project has the project accession CAJVAM000000000. This version of the project (01) has the accession number CAJVAM010000000, and consists of sequences CAJVAM010000001-CAJVAM010000079. The assembly iyEctLitu1.1 is based on 110x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..79 /organism="Ectemnius lituratus" /mol_type="genomic DNA" /db_xref="taxon:2495015" WGS CAJVAM010000001-CAJVAM010000079 // LOCUS CAJUUR010000000 26 rc DNA linear INV 06-JUL-2021 DEFINITION Chrysoteuchia culmella, whole genome shotgun sequencing project. ACCESSION CAJUUR000000000 VERSION CAJUUR000000000.1 DBLINK BioProject: PRJEB45323 BioSample: SAMEA7701502 KEYWORDS WGS. SOURCE Chrysoteuchia culmella ORGANISM Chrysoteuchia culmella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pyraloidea; Crambidae; Crambinae; Chrysoteuchia. REFERENCE 1 (bases 1 to 26) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysoteuchia culmella whole genome shotgun (WGS) project has the project accession CAJUUR000000000. This version of the project (01) has the accession number CAJUUR010000000, and consists of sequences CAJUUR010000001-CAJUUR010000026. The assembly ilChrCulm1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..26 /organism="Chrysoteuchia culmella" /mol_type="genomic DNA" /db_xref="taxon:1594250" WGS CAJUUR010000001-CAJUUR010000026 // LOCUS CAJUZJ010000000 12 rc DNA linear INV 06-JUL-2021 DEFINITION Lineus longissimus, whole genome shotgun sequencing project. ACCESSION CAJUZJ000000000 VERSION CAJUZJ000000000.1 DBLINK BioProject: PRJEB45696 BioSample: SAMEA7522833 KEYWORDS WGS. SOURCE Lineus longissimus ORGANISM Lineus longissimus Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Nemertea; Pilidiophora; Heteronemertea; Lineidae; Lineus. REFERENCE 1 (bases 1 to 12) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Lineus longissimus whole genome shotgun (WGS) project has the project accession CAJUZJ000000000. This version of the project (01) has the accession number CAJUZJ010000000, and consists of sequences CAJUZJ010000001-CAJUZJ010000012. The assembly tnLinLong1.1 is based on 79x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Chromosome 5 contains a large inversion between sister chromatids at approximately 11.1-15.4Mb. FEATURES Location/Qualifiers source 1..12 /organism="Lineus longissimus" /mol_type="genomic DNA" /db_xref="taxon:88925" WGS CAJUZJ010000001-CAJUZJ010000012 // LOCUS CAJUZF010000000 9 rc DNA linear INV 06-JUL-2021 DEFINITION Ypsolopha scabrella, whole genome shotgun sequencing project. ACCESSION CAJUZF000000000 VERSION CAJUZF000000000.1 DBLINK BioProject: PRJEB45691 BioSample: SAMEA7701504 KEYWORDS WGS. SOURCE Ypsolopha scabrella ORGANISM Ypsolopha scabrella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Yponomeutoidea; Ypsolophidae; Ypsolopha. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ypsolopha scabrella whole genome shotgun (WGS) project has the project accession CAJUZF000000000. This version of the project (01) has the accession number CAJUZF010000000, and consists of sequences CAJUZF010000001-CAJUZF010000009. The assembly ilYpsScab1.1 is based on 17x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..9 /organism="Ypsolopha scabrella" /mol_type="genomic DNA" /db_xref="taxon:1870435" WGS CAJUZF010000001-CAJUZF010000009 // LOCUS CAJUUH010000000 7 rc DNA linear INV 06-JUL-2021 DEFINITION Bembecia ichneumoniformis, whole genome shotgun sequencing project. ACCESSION CAJUUH000000000 VERSION CAJUUH000000000.1 DBLINK BioProject: PRJEB45319 BioSample: SAMEA7701282 KEYWORDS WGS. SOURCE Bembecia ichneumoniformis (six-belted clearwing) ORGANISM Bembecia ichneumoniformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sesioidea; Sesiidae; Sesiinae; Synanthedonini; Bembecia. REFERENCE 1 (bases 1 to 7) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Bembecia ichneumoniformis whole genome shotgun (WGS) project has the project accession CAJUUH000000000. This version of the project (01) has the accession number CAJUUH010000000, and consists of sequences CAJUUH010000001-CAJUUH010000007. The assembly ilBemIchn1.1 is based on 30x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..7 /organism="Bembecia ichneumoniformis" /mol_type="genomic DNA" /db_xref="taxon:301037" WGS CAJUUH010000001-CAJUUH010000007 // LOCUS CAJUUV010000000 5 rc DNA linear VRT 06-JUL-2021 DEFINITION Taurulus bubalis, whole genome shotgun sequencing project. ACCESSION CAJUUV000000000 VERSION CAJUUV000000000.1 DBLINK BioProject: PRJEB45317 BioSample: SAMEA7522994 KEYWORDS WGS. SOURCE Taurulus bubalis ORGANISM Taurulus bubalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Perciformes; Cottioidei; Cottales; Cottidae; Taurulus. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Taurulus bubalis whole genome shotgun (WGS) project has the project accession CAJUUV000000000. This version of the project (01) has the accession number CAJUUV010000000, and consists of sequences CAJUUV010000001-CAJUUV010000005. The assembly fTauBub2.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Taurulus bubalis" /mol_type="genomic DNA" /db_xref="taxon:61643" WGS CAJUUV010000001-CAJUUV010000005 // LOCUS CAJUUG010000000 5 rc DNA linear INV 06-JUL-2021 DEFINITION Ennomos quercinarius, whole genome shotgun sequencing project. ACCESSION CAJUUG000000000 VERSION CAJUUG000000000.1 DBLINK BioProject: PRJEB45324 BioSample: SAMEA7701560 KEYWORDS WGS. SOURCE Ennomos quercinarius ORGANISM Ennomos quercinarius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Ennomos. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ennomos quercinarius whole genome shotgun (WGS) project has the project accession CAJUUG000000000. This version of the project (01) has the accession number CAJUUG010000000, and consists of sequences CAJUUG010000001-CAJUUG010000005. The assembly ilEnnQuei1.1 is based on 47x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Ennomos quercinarius" /mol_type="genomic DNA" /db_xref="taxon:875883" WGS CAJUUG010000001-CAJUUG010000005 // LOCUS CAJVCG010000000 2 rc DNA linear INV 06-JUL-2021 DEFINITION Amphipyra berbera, whole genome shotgun sequencing project. ACCESSION CAJVCG000000000 VERSION CAJVCG000000000.1 DBLINK BioProject: PRJEB45915 BioSample: SAMEA7701493 KEYWORDS WGS. SOURCE Amphipyra berbera ORGANISM Amphipyra berbera Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Amphipyrinae; Amphipyra. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (25-JUN-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Amphipyra berbera whole genome shotgun (WGS) project has the project accession CAJVCG000000000. This version of the project (01) has the accession number CAJVCG010000000, and consists of sequences CAJVCG010000001-CAJVCG010000002. The assembly ilAmpBerb1.1 is based on 41x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Amphipyra berbera" /mol_type="genomic DNA" /db_xref="taxon:987877" WGS CAJVCG010000001-CAJVCG010000002 // LOCUS CAJUUF010000000 2 rc DNA linear INV 06-JUL-2021 DEFINITION Parapoynx stratiotata, whole genome shotgun sequencing project. ACCESSION CAJUUF000000000 VERSION CAJUUF000000000.1 DBLINK BioProject: PRJEB45330 BioSample: SAMEA7519920 KEYWORDS WGS. SOURCE Parapoynx stratiotata ORGANISM Parapoynx stratiotata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pyraloidea; Crambidae; Nymphulinae; Parapoynx. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Parapoynx stratiotata whole genome shotgun (WGS) project has the project accession CAJUUF000000000. This version of the project (01) has the accession number CAJUUF010000000, and consists of sequences CAJUUF010000001-CAJUUF010000002. The assembly ilParStra1.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Parapoynx stratiotata" /mol_type="genomic DNA" /db_xref="taxon:1594321" WGS CAJUUF010000001-CAJUUF010000002 // LOCUS CAJUUD010000000 1 rc DNA linear INV 06-JUL-2021 DEFINITION Carcina quercana, whole genome shotgun sequencing project. ACCESSION CAJUUD000000000 VERSION CAJUUD000000000.1 DBLINK BioProject: PRJEB45321 BioSample: SAMEA7519850 KEYWORDS WGS. SOURCE Carcina quercana ORGANISM Carcina quercana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Gelechioidea; Peleopodidae; Carcina. REFERENCE 1 (bases 1 to 1) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Carcina quercana whole genome shotgun (WGS) project has the project accession CAJUUD000000000. This version of the project (01) has the accession number CAJUUD010000000, and consists of sequence CAJUUD010000001. The assembly ilCarQuer1.1 is based on 57x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1 /organism="Carcina quercana" /mol_type="genomic DNA" /db_xref="taxon:116121" /note="contig: scaffold_42_ctg1" WGS CAJUUD010000001 // LOCUS CAJUUK010000000 1 rc DNA linear INV 06-JUL-2021 DEFINITION Noctua janthe, whole genome shotgun sequencing project. ACCESSION CAJUUK000000000 VERSION CAJUUK000000000.1 DBLINK BioProject: PRJEB45329 BioSample: SAMEA7701537 KEYWORDS WGS. SOURCE Noctua janthe ORGANISM Noctua janthe Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Noctua. REFERENCE 1 (bases 1 to 1) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (27-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Noctua janthe whole genome shotgun (WGS) project has the project accession CAJUUK000000000. This version of the project (01) has the accession number CAJUUK010000000, and consists of sequence CAJUUK010000001. The assembly ilNocJant1.1 is based on 48x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1 /organism="Noctua janthe" /mol_type="genomic DNA" /db_xref="taxon:987995" /note="contig: scaffold_38_ctg1" WGS CAJUUK010000001 // LOCUS JAHRHI010000000 937 rc DNA linear ENV 03-JUL-2021 DEFINITION MAG: Wolbachia endosymbiont of Pissodes strobi isolate WGEN-1, whole genome shotgun sequencing project. ACCESSION JAHRHI000000000 VERSION JAHRHI000000000.1 DBLINK BioProject: PRJNA588625 BioSample: SAMN19814495 KEYWORDS WGS; Metagenome Assembled Genome; MAG. SOURCE Wolbachia endosymbiont of Pissodes strobi (symbiont metagenome) ORGANISM Wolbachia endosymbiont of Pissodes strobi Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Wolbachieae; Wolbachia; unclassified Wolbachia. REFERENCE 1 (bases 1 to 937) AUTHORS Whitehill,J.G.A., Gagalova,K., Yuen,M.S., Culibrk,L., Lin,D., Keeling,C., Coombe,L., Jackman,S.D., Warren,R.L., Ritland,C., Birol,I., Bohlmann,J. and Jones,S.J.M. TITLE Genome size expansion in a forest insect pest, the weevil Pissodes strobi, and signatures of a Wolbachia bacterial endosymbiont JOURNAL Unpublished REFERENCE 2 (bases 1 to 937) AUTHORS Whitehill,J.G.A., Gagalova,K., Yuen,M.S., Culibrk,L., Lin,D., Keeling,C., Coombe,L., Jackman,S.D., Warren,R.L., Ritland,C., Birol,I., Bohlmann,J. and Jones,S.J.M. TITLE Direct Submission JOURNAL Submitted (23-JUN-2021) Canada's Michael Smith Genome Sciences Centre, BC Cancer, 570 7th Ave, Vancouver, British Columbia V5Z 4S6, Canada COMMENT The Wolbachia endosymbiont of Pissodes strobi whole genome shotgun (WGS) project has the project accession JAHRHI000000000. This version of the project (01) has the accession number JAHRHI010000000, and consists of sequences JAHRHI010000001-JAHRHI010000937. Bacteria and source DNA available from Jorg Bohlmann, UBC. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Assembly-Data-START## Assembly Date :: JUN-2019 Assembly Method :: ABySS v. 2.0 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 230.0x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 06/28/2021 10:42:35 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision :: 5.2 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 1,717 CDSs (total) :: 1,670 Genes (coding) :: 1,550 CDSs (with protein) :: 1,550 Genes (RNA) :: 47 rRNAs :: 2, 3, 3 (5S, 16S, 23S) complete rRNAs :: 2, 1, 1 (5S, 16S, 23S) partial rRNAs :: 2, 2 (16S, 23S) tRNAs :: 35 ncRNAs :: 4 Pseudo Genes (total) :: 120 CDSs (without protein) :: 120 Pseudo Genes (ambiguous residues) :: 0 of 120 Pseudo Genes (frameshifted) :: 49 of 120 Pseudo Genes (incomplete) :: 84 of 120 Pseudo Genes (internal stop) :: 6 of 120 Pseudo Genes (multiple problems) :: 17 of 120 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..937 /organism="Wolbachia endosymbiont of Pissodes strobi" /mol_type="genomic DNA" /isolate="WGEN-1" /host="Pissodes strobi" /db_xref="taxon:2832337" /environmental_sample /country="Canada: British Columbia" /lat_lon="49.264800 N 123.116850 W" /collection_date="2019-11-10" /metagenome_source="symbiont metagenome" /note="metagenomic" WGS JAHRHI010000001-JAHRHI010000937 // LOCUS JADKXX010000000 29147 rc DNA linear VRT 01-JUL-2021 DEFINITION Butorides virescens isolate ROMO101590, whole genome shotgun sequencing project. ACCESSION JADKXX000000000 VERSION JADKXX000000000.1 DBLINK BioProject: PRJNA666735 BioSample: SAMN16326460 KEYWORDS WGS. SOURCE Butorides virescens (green heron) ORGANISM Butorides virescens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Pelecaniformes; Ardeidae; Butorides. REFERENCE 1 (bases 1 to 29147) AUTHORS Culibrk,L., Ashkani,J., Haddrath,O., Paton,T., Scherer,S., Aziz,N. and Jones,S.J. TITLE Genome sequencing and assembly of Green Heron (Butorides virescens) JOURNAL Unpublished REFERENCE 2 (bases 1 to 29147) AUTHORS Culibrk,L., Ashkani,J., Haddrath,O., Paton,T., Scherer,S., Aziz,N. and Jones,S.J. TITLE Direct Submission JOURNAL Submitted (03-NOV-2020) Genome Sciences Centre, GSC CanSeq, 570 West 7th Avenue, Vancouver, BC V5Z 4E6, Canada COMMENT The Butorides virescens whole genome shotgun (WGS) project has the project accession JADKXX000000000. This version of the project (01) has the accession number JADKXX010000000, and consists of sequences JADKXX010000001-JADKXX010029147. ##Genome-Assembly-Data-START## Assembly Method :: Supernova v. 2.1.1 Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 53.0x Sequencing Technology :: HiSeq X ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..29147 /organism="Butorides virescens" /mol_type="genomic DNA" /isolate="ROMO101590" /specimen_voucher="1B-4519" /db_xref="taxon:110671" /sex="male" /tissue_type="Unspecified mixture of tissues" /dev_stage="adult" /country="Canada: Whitby, Ontario" /collection_date="2005-08-07" WGS JADKXX010000001-JADKXX010029147 // LOCUS JAHNUP010000000 2643 rc DNA linear INV 29-JUN-2021 DEFINITION Amphibalanus amphitrite isolate SeventyFive, whole genome shotgun sequencing project. ACCESSION JAHNUP000000000 VERSION JAHNUP000000000.1 DBLINK BioProject: PRJNA734913 BioSample: SAMN19549327 KEYWORDS WGS. SOURCE Amphibalanus amphitrite ORGANISM Amphibalanus amphitrite Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Multicrustacea; Hexanauplia; Cirripedia; Thoracica; Sessilia; Balanidae; Amphibalanus. REFERENCE 1 (bases 1 to 2643) AUTHORS Schultzhaus,J., Hervey,J., Smerchansky,M., Taitt,C., Leary,D., Bernot,J., Avdeyev,P., Orihuela,B., Crandall,K., Rittschof,D., Wahl,K. and Spillmann,C. TITLE A Reference genome of the acorn barnacle Amphibalanus amphitrite JOURNAL Unpublished REFERENCE 2 (bases 1 to 2643) AUTHORS Schultzhaus,J., Hervey,J., Smerchansky,M., Taitt,C., Leary,D., Bernot,J., Avdeyev,P., Orihuela,B., Crandall,K., Rittschof,D., Wahl,K. and Spillmann,C. TITLE Direct Submission JOURNAL Submitted (15-JUN-2021) NRL-DC, Naval Research Laboratory, 4555 Overlook Avenue - SW, Washington, DC 20375, USA COMMENT The Amphibalanus amphitrite whole genome shotgun (WGS) project has the project accession JAHNUP000000000. This version of the project (01) has the accession number JAHNUP010000000, and consists of sequences JAHNUP010000001-JAHNUP010002643. ##Genome-Assembly-Data-START## Assembly Date :: 10-DEC-2019 Assembly Method :: FALCON-Unzip v. 0.3.4 Assembly Name :: NRLGWU_Aamphi_draft Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 79.7x Sequencing Technology :: PacBio; Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2643 /organism="Amphibalanus amphitrite" /mol_type="genomic DNA" /isolate="SeventyFive" /isolation_source="Laboratory cultivated, inbred" /db_xref="taxon:1232801" /tissue_type="Body" /country="USA" /collection_date="2018-07-23" WGS JAHNUP010000001-JAHNUP010002643 // LOCUS CAJQFV010000000 1100 rc DNA linear INV 14-APR-2021 DEFINITION Autographa pulchrina, whole genome shotgun sequencing project. ACCESSION CAJQFV000000000 VERSION CAJQFV000000000.1 DBLINK BioProject: PRJEB44049 BioSample: SAMEA7520527 KEYWORDS WGS. SOURCE Autographa pulchrina ORGANISM Autographa pulchrina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Plusiinae; Autographa. REFERENCE 1 (bases 1 to 1100) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Autographa pulchrina whole genome shotgun (WGS) project has the project accession CAJQFV000000000. This version of the project (01) has the accession number CAJQFV010000000, and consists of sequences CAJQFV010000001-CAJQFV010001100. The assembly ilAutPulc1.1 is based on 47x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1100 /organism="Autographa pulchrina" /mol_type="genomic DNA" /db_xref="taxon:987893" WGS CAJQFV010000001-CAJQFV010001100 // LOCUS JAHDTO010000000 5410 rc DNA linear VRT 24-MAY-2021 DEFINITION Alosa sapidissima isolate fAloSap1, whole genome shotgun sequencing project. ACCESSION JAHDTO000000000 VERSION JAHDTO000000000.1 DBLINK BioProject: PRJNA728146 BioSample: SAMN18857608 KEYWORDS WGS. SOURCE Alosa sapidissima (American shad) ORGANISM Alosa sapidissima Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Clupei; Clupeiformes; Clupeoidei; Clupeidae; Alosa. REFERENCE 1 (bases 1 to 5410) AUTHORS Therkildsen,N.O., Tigano,A., Formenti,G., Hyle,R., Mountcastle,J., Balacco,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Alosa sapidissima (American shade) genome, fAloSap1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 5410) AUTHORS Therkildsen,N.O., Tigano,A., Formenti,G., Hyle,R., Mountcastle,J., Balacco,J., Tracey,A., Sims,Y., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (15-MAY-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Alosa sapidissima whole genome shotgun (WGS) project has the project accession JAHDTO000000000. This version of the project (01) has the accession number JAHDTO010000000, and consists of sequences JAHDTO010000001-JAHDTO010005410. ##Genome-Assembly-Data-START## Assembly Date :: 21-APR-2021 Assembly Method :: Hifisam v. 0.14; Purge_dups v. 1.0.1; Salsa v. 2.2; Scaff10X v. 3.2.1; Bionano Solve v. 3.6.1; VGP pipeline v. 2.0; gEVAL manual curation v. 2021-04-21 Assembly Name :: fAloSap1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 33.0x Sequencing Technology :: PacBio Sequel II HiFi; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..5410 /organism="Alosa sapidissima" /mol_type="genomic DNA" /isolate="fAloSap1" /specimen_voucher="AsapiF_1" /db_xref="taxon:34773" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="USA: St. Johns River, Florida" /lat_lon="28.438892 N 81.894728 W" /collection_date="2020-02-07" /collected_by="Reid Hyle" WGS JAHDTO010000001-JAHDTO010005410 // LOCUS JAHDTN010000000 73 rc DNA linear VRT 25-MAY-2021 DEFINITION Alosa sapidissima isolate fAloSap1, whole genome shotgun sequencing project. ACCESSION JAHDTN000000000 VERSION JAHDTN000000000.1 DBLINK BioProject: PRJNA728145 BioSample: SAMN18857608 KEYWORDS WGS. SOURCE Alosa sapidissima (American shad) ORGANISM Alosa sapidissima Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Clupei; Clupeiformes; Clupeoidei; Clupeidae; Alosa. REFERENCE 1 (bases 1 to 73) AUTHORS Therkildsen,N.O., Tigano,A., Formenti,G., Hyle,R., Mountcastle,J., Balacco,J., Tracey,A., Sims,Y., Howe,K., Federigo,O. and Jarvis,E.D. TITLE Alosa sapidissima (American shade) genome, fAloSap1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 73) AUTHORS Therkildsen,N.O., Tigano,A., Formenti,G., Hyle,R., Mountcastle,J., Balacco,J., Tracey,A., Sims,Y., Howe,K., Federigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (15-MAY-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Alosa sapidissima whole genome shotgun (WGS) project has the project accession JAHDTN000000000. This version of the project (01) has the accession number JAHDTN010000000, and consists of sequences JAHDTN010000001-JAHDTN010000073. ##Genome-Assembly-Data-START## Assembly Date :: 21-APR-2021 Assembly Method :: Hifisam v. 0.14; Purge_dups v. 1.0.1; Salsa v. 2.2; Scaff10X v. 3.2.1; Bionano Solve v. 3.6.1; VGP pipeline v. 2.0; gEVAL manual curation v. 2021-04-21 Assembly Name :: fAloSap1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 33.0x Sequencing Technology :: PacBio Sequel II HiFi; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..73 /organism="Alosa sapidissima" /mol_type="genomic DNA" /isolate="fAloSap1" /specimen_voucher="AsapiF_1" /db_xref="taxon:34773" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="USA: St. Johns River, Florida" /lat_lon="28.438892 N 81.894728 W" /collection_date="2020-02-07" /collected_by="Reid Hyle" WGS JAHDTN010000001-JAHDTN010000073 WGS_SCAFLD CM031716-CM031739 // LOCUS VCHM03000000 1590 rc DNA linear VRT 25-MAY-2021 DEFINITION Reinhardtius hippoglossoides isolate HD-2018-mb, whole genome shotgun sequencing project. ACCESSION VCHM00000000 VERSION VCHM00000000.3 DBLINK BioProject: PRJNA499109 BioSample: SAMN11811143 KEYWORDS WGS. SOURCE Reinhardtius hippoglossoides (Greenland flounder) ORGANISM Reinhardtius hippoglossoides Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Carangaria; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Reinhardtius. REFERENCE 1 (bases 1 to 1590) AUTHORS Ferchaud,A.-L., Normandeau,E., Djambazian,H., Ragoussis,I. and Bernatchez,L. TITLE Genome assembly of Greenland Halibut reveals a recent genetic sex determinism JOURNAL Unpublished REFERENCE 2 (bases 1 to 1590) AUTHORS Djambazian,H. TITLE Direct Submission JOURNAL Submitted (04-DEC-2018) Human Genetics, McGill University, 740 Doctor Penfield, Montreal, Quebec H3A 0G1, Canada REFERENCE 3 (bases 1 to 1590) AUTHORS Ferchaud,A.-L., Normandeau,E., Djambazian,H., Ragoussis,I. and Bernatchez,L. TITLE Direct Submission JOURNAL Submitted (23-FEB-2021) Departement de Biologie, Universite Laval, 1030 Avenue de la Medecine, Quebec G1V0A6, Canada COMMENT On May 19, 2021 this sequence version replaced VCHM00000000.2. The Reinhardtius hippoglossoides whole genome shotgun (WGS) project has the project accession VCHM00000000. This version of the project (03) has the accession number VCHM03000000, and consists of sequences VCHM03000001-VCHM03001590. ##Genome-Assembly-Data-START## Assembly Date :: 20-NOV-2020 Assembly Method :: wtdbg2 v. 2.5; Dovetail (Hi-C) v. 2018-08 Assembly Name :: UL_REHI_2.0 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1590 /organism="Reinhardtius hippoglossoides" /mol_type="genomic DNA" /isolate="HD-2018-mb" /db_xref="taxon:111784" /sex="female" /tissue_type="muscle, blood" /dev_stage="Mature" /ecotype="Greenland" WGS VCHM03000001-VCHM03001590 WGS_SCAFLD CM031670-CM031693 // LOCUS OFHY04000000 363 rc DNA linear VRT 23-APR-2021 DEFINITION Astatotilapia calliptera, whole genome shotgun sequencing project. ACCESSION OFHY00000000 VERSION OFHY00000000.4 DBLINK BioProject: PRJEB24325 BioSample: SAMEA104026430 KEYWORDS WGS. SOURCE Astatotilapia calliptera (eastern happy) ORGANISM Astatotilapia calliptera Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini; Astatotilapia. REFERENCE 1 AUTHORS Datahose. TITLE Direct Submission JOURNAL Submitted (10-JAN-2018) SC, Wellcome Trust Sanger Institute, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 363) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (16-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced OFHY00000000.3. The Astatotilapia calliptera whole genome shotgun (WGS) project has the project accession OFHY00000000. This version of the project (04) has the accession number OFHY04000000, and consists of sequences OFHY04000001-OFHY04000363. The assembly fAstCal1.3 is based on 48x PacBio RSII data, 112x Illumina HiSeqX data generated from a 10X Genomics Chromium library, and single-enzyme BioNano Irys data. An initial PacBio assembly was made using Falcon-unzip and the primary contigs extended by merging with a miniasm assembly. The contigs were then scaffolded using the 10X data with scaff10x. After using the PacBio data to gap fill with PBJelly and polish with Quiver, the assembly was manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano data. The assembly was then polished again using the 10X Illumina data and freebayes. Two genetic maps [PMID: 23622422, 25156298] were used to allocate scaffolds to chromosomes, followed by further curation and verification using gEVAL. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. FEATURES Location/Qualifiers source 1..363 /organism="Astatotilapia calliptera" /mol_type="genomic DNA" /db_xref="taxon:8154" WGS OFHY04000001-OFHY04000363 WGS_SCAFLD LS420019-LS420040 // LOCUS CAJSMG010000000 2079 rc DNA linear INV 19-MAY-2021 DEFINITION Volucella inanis, whole genome shotgun sequencing project. ACCESSION CAJSMG000000000 VERSION CAJSMG000000000.1 DBLINK BioProject: PRJEB44950 BioSample: SAMEA7520171 KEYWORDS WGS. SOURCE Volucella inanis ORGANISM Volucella inanis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Volucellini; Volucella. REFERENCE 1 (bases 1 to 2079) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Volucella inanis whole genome shotgun (WGS) project has the project accession CAJSMG000000000. This version of the project (01) has the accession number CAJSMG010000000, and consists of sequences CAJSMG010000001-CAJSMG010002079. The assembly idVolInan1.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2079 /organism="Volucella inanis" /mol_type="genomic DNA" /db_xref="taxon:226151" WGS CAJSMG010000001-CAJSMG010002079 // LOCUS CAJSMD010000000 1813 rc DNA linear INV 19-MAY-2021 DEFINITION Eristalis pertinax, whole genome shotgun sequencing project. ACCESSION CAJSMD000000000 VERSION CAJSMD000000000.1 DBLINK BioProject: PRJEB44949 BioSample: SAMEA7520039 KEYWORDS WGS. SOURCE Eristalis pertinax ORGANISM Eristalis pertinax Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Eristalini; Eristalis. REFERENCE 1 (bases 1 to 1813) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eristalis pertinax whole genome shotgun (WGS) project has the project accession CAJSMD000000000. This version of the project (01) has the accession number CAJSMD010000000, and consists of sequences CAJSMD010000001-CAJSMD010001813. The assembly idEriPert2.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Y chromosome identified by absence of read mapping from female sample idEriPert1. FEATURES Location/Qualifiers source 1..1813 /organism="Eristalis pertinax" /mol_type="genomic DNA" /db_xref="taxon:1572519" WGS CAJSMD010000001-CAJSMD010001813 // LOCUS CAJSLZ010000000 315 rc DNA linear INV 19-MAY-2021 DEFINITION Idaea aversata, whole genome shotgun sequencing project. ACCESSION CAJSLZ000000000 VERSION CAJSLZ000000000.1 DBLINK BioProject: PRJEB44946 BioSample: SAMEA7519834 KEYWORDS WGS. SOURCE Idaea aversata ORGANISM Idaea aversata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Sterrhinae; Idaea. REFERENCE 1 (bases 1 to 315) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Idaea aversata whole genome shotgun (WGS) project has the project accession CAJSLZ000000000. This version of the project (01) has the accession number CAJSLZ010000000, and consists of sequences CAJSLZ010000001-CAJSLZ010000315. The assembly ilIdaAver1.1 is based on 56x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..315 /organism="Idaea aversata" /mol_type="genomic DNA" /db_xref="taxon:104447" WGS CAJSLZ010000001-CAJSLZ010000315 // LOCUS CAJSMB010000000 282 rc DNA linear INV 19-MAY-2021 DEFINITION Crocallis elinguaria, whole genome shotgun sequencing project. ACCESSION CAJSMB000000000 VERSION CAJSMB000000000.1 DBLINK BioProject: PRJEB44954 BioSample: SAMEA7701527 KEYWORDS WGS. SOURCE Crocallis elinguaria ORGANISM Crocallis elinguaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Crocallis. REFERENCE 1 (bases 1 to 282) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Crocallis elinguaria whole genome shotgun (WGS) project has the project accession CAJSMB000000000. This version of the project (01) has the accession number CAJSMB010000000, and consists of sequences CAJSMB010000001-CAJSMB010000282. The assembly ilCroElin1.1 is based on 44x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..282 /organism="Crocallis elinguaria" /mol_type="genomic DNA" /db_xref="taxon:934829" WGS CAJSMB010000001-CAJSMB010000282 // LOCUS CAJSMA010000000 496 rc DNA linear INV 19-MAY-2021 DEFINITION Blastobasis adustella, whole genome shotgun sequencing project. ACCESSION CAJSMA000000000 VERSION CAJSMA000000000.1 DBLINK BioProject: PRJEB44952 BioSample: SAMEA7520179 KEYWORDS WGS. SOURCE Blastobasis adustella ORGANISM Blastobasis adustella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Gelechioidea; Blastobasidae; Blastobasis. REFERENCE 1 (bases 1 to 496) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Blastobasis adustella whole genome shotgun (WGS) project has the project accession CAJSMA000000000. This version of the project (01) has the accession number CAJSMA010000000, and consists of sequences CAJSMA010000001-CAJSMA010000496. The assembly ilBlaAdus2.1 is based on 50x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..496 /organism="Blastobasis adustella" /mol_type="genomic DNA" /db_xref="taxon:1869501" WGS CAJSMA010000001-CAJSMA010000496 // LOCUS CAJSMF010000000 249 rc DNA linear INV 19-MAY-2021 DEFINITION Eristalis pertinax, whole genome shotgun sequencing project. ACCESSION CAJSMF000000000 VERSION CAJSMF000000000.1 DBLINK BioProject: PRJEB44948 BioSample: SAMEA7520039 KEYWORDS WGS. SOURCE Eristalis pertinax ORGANISM Eristalis pertinax Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Eristalini; Eristalis. REFERENCE 1 (bases 1 to 249) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Eristalis pertinax whole genome shotgun (WGS) project has the project accession CAJSMF000000000. This version of the project (01) has the accession number CAJSMF010000000, and consists of sequences CAJSMF010000001-CAJSMF010000249. The assembly idEriPert2.1 is based on 29x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Y chromosome identified by absence of read mapping from female sample idEriPert1. FEATURES Location/Qualifiers source 1..249 /organism="Eristalis pertinax" /mol_type="genomic DNA" /db_xref="taxon:1572519" WGS CAJSMF010000001-CAJSMF010000249 // LOCUS CAJSME010000000 9 rc DNA linear INV 19-MAY-2021 DEFINITION Blastobasis adustella, whole genome shotgun sequencing project. ACCESSION CAJSME000000000 VERSION CAJSME000000000.1 DBLINK BioProject: PRJEB44953 BioSample: SAMEA7520179 KEYWORDS WGS. SOURCE Blastobasis adustella ORGANISM Blastobasis adustella Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Gelechioidea; Blastobasidae; Blastobasis. REFERENCE 1 (bases 1 to 9) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Blastobasis adustella whole genome shotgun (WGS) project has the project accession CAJSME000000000. This version of the project (01) has the accession number CAJSME010000000, and consists of sequences CAJSME010000001-CAJSME010000009. The assembly ilBlaAdus2.1 is based on 50x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..9 /organism="Blastobasis adustella" /mol_type="genomic DNA" /db_xref="taxon:1869501" WGS CAJSME010000001-CAJSME010000009 // LOCUS CAJSMC010000000 7 rc DNA linear INV 19-MAY-2021 DEFINITION Crocallis elinguaria, whole genome shotgun sequencing project. ACCESSION CAJSMC000000000 VERSION CAJSMC000000000.1 DBLINK BioProject: PRJEB44955 BioSample: SAMEA7701527 KEYWORDS WGS. SOURCE Crocallis elinguaria ORGANISM Crocallis elinguaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Crocallis. REFERENCE 1 (bases 1 to 7) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Crocallis elinguaria whole genome shotgun (WGS) project has the project accession CAJSMC000000000. This version of the project (01) has the accession number CAJSMC010000000, and consists of sequences CAJSMC010000001-CAJSMC010000007. The assembly ilCroElin1.1 is based on 44x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..7 /organism="Crocallis elinguaria" /mol_type="genomic DNA" /db_xref="taxon:934829" WGS CAJSMC010000001-CAJSMC010000007 // LOCUS CAJSMH010000000 46 rc DNA linear INV 19-MAY-2021 DEFINITION Volucella inanis, whole genome shotgun sequencing project. ACCESSION CAJSMH000000000 VERSION CAJSMH000000000.1 DBLINK BioProject: PRJEB44951 BioSample: SAMEA7520171 KEYWORDS WGS. SOURCE Volucella inanis ORGANISM Volucella inanis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Volucellini; Volucella. REFERENCE 1 (bases 1 to 46) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (14-MAY-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Volucella inanis whole genome shotgun (WGS) project has the project accession CAJSMH000000000. This version of the project (01) has the accession number CAJSMH010000000, and consists of sequences CAJSMH010000001-CAJSMH010000046. The assembly idVolInan1.1 is based on 26x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..46 /organism="Volucella inanis" /mol_type="genomic DNA" /db_xref="taxon:226151" WGS CAJSMH010000001-CAJSMH010000046 // LOCUS CAJRAJ010000000 13348 rc DNA linear INV 11-MAY-2021 DEFINITION Dolomedes plantarius, whole genome shotgun sequencing project. ACCESSION CAJRAJ000000000 VERSION CAJRAJ000000000.1 DBLINK BioProject: PRJEB44428 BioSample: SAMEA994727 KEYWORDS WGS. SOURCE Dolomedes plantarius ORGANISM Dolomedes plantarius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Lycosoidea; Pisauridae; Dolomedes. REFERENCE 1 (bases 1 to 13348) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Dolomedes plantarius whole genome shotgun (WGS) project has the project accession CAJRAJ000000000. This version of the project (01) has the accession number CAJRAJ010000000, and consists of sequences CAJRAJ010000001-CAJRAJ010013348. The assembly qDolPla1.1 is based on 55x PacBio data and 39x 10X Genomics Chromium data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with purge_dups, 10X based scaffolding with scaff10x, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. FEATURES Location/Qualifiers source 1..13348 /organism="Dolomedes plantarius" /mol_type="genomic DNA" /db_xref="taxon:257759" WGS CAJRAJ010000001-CAJRAJ010013348 // LOCUS CAJHNH020000000 8586 rc DNA linear INV 11-MAY-2021 DEFINITION Candidula unifasciata, whole genome shotgun sequencing project. ACCESSION CAJHNH000000000 VERSION CAJHNH000000000.2 DBLINK BioProject: PRJEB41346 BioSample: SAMEA7574008 Sequence Read Archive: ERR5838591, ERR5838592, ERR5838593, ERR5838594, ERR5838595, ERR5838596, ERR5838597, ERR5838598, ERR5838605, ERR5838606, ERR5841713, ERR5845218, ERR5845219 KEYWORDS WGS. SOURCE Candidula unifasciata ORGANISM Candidula unifasciata Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Gastropoda; Heterobranchia; Euthyneura; Panpulmonata; Eupulmonata; Stylommatophora; Helicina; Helicoidea; Geomitridae; Candidula. REFERENCE 1 (bases 1 to 8586) CONSRTM Molecular Ecology Group TITLE Direct Submission JOURNAL Submitted (16-NOV-2020) Senckenber Biodiversity and Climate Research Centre Frankfurt, Molecular Ecology Group, Georg-Voigt-Strasse 14-16, DE-60325, Frankfurt am Main, Germany REFERENCE 2 (bases 1 to 8586) CONSRTM Molecular Ecology Group TITLE Direct Submission JOURNAL Submitted (29-APR-2021) Senckenber Biodiversity and Climate Research Centre Frankfurt, Molecular Ecology Group, Georg-Voigt-Strasse 14-16, DE-60325, Frankfurt am Main, Germany COMMENT On May 16, 2021 this sequence version replaced CAJHNH000000000.1. The Candidula unifasciata whole genome shotgun (WGS) project has the project accession CAJHNH000000000. This version of the project (02) has the accession number CAJHNH020000000, and consists of sequences CAJHNH020000001-CAJHNH020008586. Here we present the draft genome sequence of the land snail Candidula unifasciata, a representative of the highly diverse Geomitridae family from western Palearctic region and Macaronesia. Analyses are based on Illumina pair-end, PacBio and Oxford Nanopore Technologies sequencing. Coverages: 120.6X for Illumnia; 25.6X for PacBio. FEATURES Location/Qualifiers source 1..8586 /organism="Candidula unifasciata" /mol_type="genomic DNA" /db_xref="taxon:100452" WGS CAJHNH020000001-CAJHNH020008586 // LOCUS CAJRAW010000000 2502 rc DNA linear VRT 11-MAY-2021 DEFINITION Caprimulgus europaeus, whole genome shotgun sequencing project. ACCESSION CAJRAW000000000 VERSION CAJRAW000000000.1 DBLINK BioProject: PRJEB44541 BioSample: SAMEA7524394 KEYWORDS WGS. SOURCE Caprimulgus europaeus (Eurasian nightjar) ORGANISM Caprimulgus europaeus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Caprimulgiformes; Caprimulgidae; Caprimulginae; Caprimulgus. REFERENCE 1 (bases 1 to 2502) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Caprimulgus europaeus whole genome shotgun (WGS) project has the project accession CAJRAW000000000. This version of the project (01) has the accession number CAJRAW010000000, and consists of sequences CAJRAW010000001-CAJRAW010002502. The assembly bCapEur3.1 is based on 87x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Arrow polishing assisted by Merfin, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2502 /organism="Caprimulgus europaeus" /mol_type="genomic DNA" /db_xref="taxon:111811" WGS CAJRAW010000001-CAJRAW010002502 // LOCUS CAJRBC010000000 3628 rc DNA linear INV 11-MAY-2021 DEFINITION Zeuzera pyrina, whole genome shotgun sequencing project. ACCESSION CAJRBC000000000 VERSION CAJRBC000000000.1 DBLINK BioProject: PRJEB44633 BioSample: SAMEA7701286 KEYWORDS WGS. SOURCE Zeuzera pyrina ORGANISM Zeuzera pyrina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Cossoidea; Cossidae; Zeuzerinae; Zeuzera. REFERENCE 1 (bases 1 to 3628) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Zeuzera pyrina whole genome shotgun (WGS) project has the project accession CAJRBC000000000. This version of the project (01) has the accession number CAJRBC010000000, and consists of sequences CAJRBC010000001-CAJRBC010003628. The assembly ilZeuPyri1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3628 /organism="Zeuzera pyrina" /mol_type="genomic DNA" /db_xref="taxon:1101072" WGS CAJRBC010000001-CAJRBC010003628 // LOCUS CAJRAG010000000 2278 rc DNA linear PLN 11-MAY-2021 DEFINITION Impatiens glandulifera, whole genome shotgun sequencing project. ACCESSION CAJRAG000000000 VERSION CAJRAG000000000.1 DBLINK BioProject: PRJEB44450 BioSample: SAMEA5248722 KEYWORDS WGS. SOURCE Impatiens glandulifera ORGANISM Impatiens glandulifera Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Balsaminaceae; Impatiens. REFERENCE 1 (bases 1 to 2278) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Impatiens glandulifera whole genome shotgun (WGS) project has the project accession CAJRAG000000000. This version of the project (01) has the accession number CAJRAG010000000, and consists of sequences CAJRAG010000001-CAJRAG010002278. The assembly dImpGla2.1 is based on 76x PacBio data, 34x 10X Genomics Chromium data, BioNano data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. FEATURES Location/Qualifiers source 1..2278 /organism="Impatiens glandulifera" /mol_type="genomic DNA" /db_xref="taxon:253017" WGS CAJRAG010000001-CAJRAG010002278 // LOCUS CAJRBD010000000 3319 rc DNA linear INV 11-MAY-2021 DEFINITION Habrosyne pyritoides, whole genome shotgun sequencing project. ACCESSION CAJRBD000000000 VERSION CAJRBD000000000.1 DBLINK BioProject: PRJEB44630 BioSample: SAMEA7701298 KEYWORDS WGS. SOURCE Habrosyne pyritoides ORGANISM Habrosyne pyritoides Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Drepanoidea; Drepanidae; Thyatirinae; Habrosyne. REFERENCE 1 (bases 1 to 3319) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Habrosyne pyritoides whole genome shotgun (WGS) project has the project accession CAJRBD000000000. This version of the project (01) has the accession number CAJRBD010000000, and consists of sequences CAJRBD010000001-CAJRBD010003319. The assembly ilHabPyri1.1 is based on 52x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..3319 /organism="Habrosyne pyritoides" /mol_type="genomic DNA" /db_xref="taxon:721137" WGS CAJRBD010000001-CAJRBD010003319 // LOCUS CAJRAE010000000 262 rc DNA linear INV 11-MAY-2021 DEFINITION Hemaris fuciformis, whole genome shotgun sequencing project. ACCESSION CAJRAE000000000 VERSION CAJRAE000000000.1 DBLINK BioProject: PRJEB44425 BioSample: SAMEA5248724 KEYWORDS WGS. SOURCE Hemaris fuciformis ORGANISM Hemaris fuciformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Sphingidae; Macroglossinae; Dilophonotini; Hemaris. REFERENCE 1 (bases 1 to 262) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Hemaris fuciformis whole genome shotgun (WGS) project has the project accession CAJRAE000000000. This version of the project (01) has the accession number CAJRAE010000000, and consists of sequences CAJRAE010000001-CAJRAE010000262. The assembly iHemFuc1.1 (alternate haplotype) is based on 88x PacBio data, 88x 10X Genomics Chromium data, and BioNano data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Solve, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. FEATURES Location/Qualifiers source 1..262 /organism="Hemaris fuciformis" /mol_type="genomic DNA" /db_xref="taxon:987953" WGS CAJRAE010000001-CAJRAE010000262 // LOCUS CAJRBA010000000 182 rc DNA linear INV 11-MAY-2021 DEFINITION Coccinella septempunctata, whole genome shotgun sequencing project. ACCESSION CAJRBA000000000 VERSION CAJRBA000000000.1 DBLINK BioProject: PRJEB44628 BioSample: SAMEA7520205 KEYWORDS WGS. SOURCE Coccinella septempunctata (seven-spotted ladybird) ORGANISM Coccinella septempunctata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Coccinella. REFERENCE 1 (bases 1 to 182) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Coccinella septempunctata whole genome shotgun (WGS) project has the project accession CAJRBA000000000. This version of the project (01) has the accession number CAJRBA010000000, and consists of sequences CAJRBA010000001-CAJRBA010000182. The assembly icCocSept1.1 is based on 76x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..182 /organism="Coccinella septempunctata" /mol_type="genomic DNA" /db_xref="taxon:41139" WGS CAJRBA010000001-CAJRBA010000182 // LOCUS CAJRBI010000000 666 rc DNA linear INV 11-MAY-2021 DEFINITION Nomada fabriciana, whole genome shotgun sequencing project. ACCESSION CAJRBI000000000 VERSION CAJRBI000000000.1 DBLINK BioProject: PRJEB44637 BioSample: SAMEA7520701 KEYWORDS WGS. SOURCE Nomada fabriciana ORGANISM Nomada fabriciana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Nomadini; Nomada. REFERENCE 1 (bases 1 to 666) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Nomada fabriciana whole genome shotgun (WGS) project has the project accession CAJRBI000000000. This version of the project (01) has the accession number CAJRBI010000000, and consists of sequences CAJRBI010000001-CAJRBI010000666. The assembly iyNomFabr1.1 is based on 99x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..666 /organism="Nomada fabriciana" /mol_type="genomic DNA" /db_xref="taxon:601510" WGS CAJRBI010000001-CAJRBI010000666 // LOCUS CAJRAK010000000 853 rc DNA linear INV 11-MAY-2021 DEFINITION Osmia bicornis bicornis, whole genome shotgun sequencing project. ACCESSION CAJRAK000000000 VERSION CAJRAK000000000.1 DBLINK BioProject: PRJEB44454 BioSample: SAMEA5248723 KEYWORDS WGS. SOURCE Osmia bicornis bicornis ORGANISM Osmia bicornis bicornis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Megachilidae; Megachilinae; Osmia. REFERENCE 1 (bases 1 to 853) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Osmia bicornis bicornis whole genome shotgun (WGS) project has the project accession CAJRAK000000000. This version of the project (01) has the accession number CAJRAK010000000, and consists of sequences CAJRAK010000001-CAJRAK010000853. The assembly iOsmBic2.1 is based on 93x PacBio data and 46x 10X Genomics Chromium data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. FEATURES Location/Qualifiers source 1..853 /organism="Osmia bicornis bicornis" /mol_type="genomic DNA" /sub_species="bicornis" /db_xref="taxon:1437191" WGS CAJRAK010000001-CAJRAK010000853 // LOCUS CAJRAB010000000 2316 rc DNA linear INV 11-MAY-2021 DEFINITION Brachyptera putata, whole genome shotgun sequencing project. ACCESSION CAJRAB000000000 VERSION CAJRAB000000000.1 DBLINK BioProject: PRJEB44420 BioSample: SAMEA5248727 KEYWORDS WGS. SOURCE Brachyptera putata ORGANISM Brachyptera putata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Polyneoptera; Plecoptera; Nemouroidea; Taeniopterygidae; Brachypterainae; Brachyptera. REFERENCE 1 (bases 1 to 2316) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Brachyptera putata whole genome shotgun (WGS) project has the project accession CAJRAB000000000. This version of the project (01) has the accession number CAJRAB010000000, and consists of sequences CAJRAB010000001-CAJRAB010002316. The assembly iBraPut3m.1 is based on 64x PacBio data and 101x 10X Genomics Chromium data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. iBraPut3m is a pool of 2 individuals (iBraBut1 and iBraPut2). PacBio data is from iBraPut3m, 10X data is from iBraPut1, and Hi-C is from another individual, iBraPut4. The assembly process included the following sequence of steps: initial PacBio assembly generation with wtdbg2, Arrow polishing with the PacBio data, FreeBayes polishing with the 10X data, 10X based scaffolding with scaff10x, Hi-C based scaffolding and curation carried out at Baylor, a further round of FreeBayes polishing with the 10X data, and retained haplotig separation with purge_dups. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2316 /organism="Brachyptera putata" /mol_type="genomic DNA" /db_xref="taxon:2065413" WGS CAJRAB010000001-CAJRAB010002316 // LOCUS CAJRAH010000000 1105 rc DNA linear PLN 11-MAY-2021 DEFINITION Impatiens glandulifera, whole genome shotgun sequencing project. ACCESSION CAJRAH000000000 VERSION CAJRAH000000000.1 DBLINK BioProject: PRJEB44449 BioSample: SAMEA5248722 KEYWORDS WGS. SOURCE Impatiens glandulifera ORGANISM Impatiens glandulifera Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Balsaminaceae; Impatiens. REFERENCE 1 (bases 1 to 1105) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Impatiens glandulifera whole genome shotgun (WGS) project has the project accession CAJRAH000000000. This version of the project (01) has the accession number CAJRAH010000000, and consists of sequences CAJRAH010000001-CAJRAH010001105. The assembly dImpGla2.1 is based on 76x PacBio data, 34x 10X Genomics Chromium data, BioNano data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding and curation carried out at Baylor, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1105 /organism="Impatiens glandulifera" /mol_type="genomic DNA" /db_xref="taxon:253017" WGS CAJRAH010000001-CAJRAH010001105 // LOCUS CAJRAL010000000 425 rc DNA linear INV 11-MAY-2021 DEFINITION Osmia bicornis bicornis, whole genome shotgun sequencing project. ACCESSION CAJRAL000000000 VERSION CAJRAL000000000.1 DBLINK BioProject: PRJEB44455 BioSample: SAMEA5248723 KEYWORDS WGS. SOURCE Osmia bicornis bicornis ORGANISM Osmia bicornis bicornis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Megachilidae; Megachilinae; Osmia. REFERENCE 1 (bases 1 to 425) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (21-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Osmia bicornis bicornis whole genome shotgun (WGS) project has the project accession CAJRAL000000000. This version of the project (01) has the accession number CAJRAL010000000, and consists of sequences CAJRAL010000001-CAJRAL010000425. The assembly iOsmBic2.1 is based on 93x PacBio data and 46x 10X Genomics Chromium data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding and curation carried out at Baylor, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..425 /organism="Osmia bicornis bicornis" /mol_type="genomic DNA" /sub_species="bicornis" /db_xref="taxon:1437191" WGS CAJRAL010000001-CAJRAL010000425 // LOCUS CABFKC020000000 278 rc DNA linear VRT 11-MAY-2021 DEFINITION Streptopelia turtur, whole genome shotgun sequencing project. ACCESSION CABFKC000000000 VERSION CABFKC000000000.2 DBLINK BioProject: PRJEB32724 BioSample: SAMEA994735 KEYWORDS WGS. SOURCE Streptopelia turtur ORGANISM Streptopelia turtur Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Streptopelia. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (24-MAY-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 278) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On May 15, 2021 this sequence version replaced CABFKC000000000.1. The Streptopelia turtur whole genome shotgun (WGS) project has the project accession CABFKC000000000. This version of the project (02) has the accession number CABFKC020000000, and consists of sequences CABFKC020000001-CABFKC020000278. The assembly bStrTur1.2 is based on 44x PacBio data, 62x coverage 10X Genomics Chromium data, and BioNano data generated at the Wellcome Sanger Institute, and 106x coverage Hi-C data generated by Arima Genomics. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny to Gallus gallus. FEATURES Location/Qualifiers source 1..278 /organism="Streptopelia turtur" /mol_type="genomic DNA" /db_xref="taxon:177155" WGS CABFKC020000001-CABFKC020000278 // LOCUS CAJRAI010000000 423 rc DNA linear INV 11-MAY-2021 DEFINITION Dolomedes plantarius, whole genome shotgun sequencing project. ACCESSION CAJRAI000000000 VERSION CAJRAI000000000.1 DBLINK BioProject: PRJEB44429 BioSample: SAMEA994727 KEYWORDS WGS. SOURCE Dolomedes plantarius ORGANISM Dolomedes plantarius Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Lycosoidea; Pisauridae; Dolomedes. REFERENCE 1 (bases 1 to 423) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Dolomedes plantarius whole genome shotgun (WGS) project has the project accession CAJRAI000000000. This version of the project (01) has the accession number CAJRAI010000000, and consists of sequences CAJRAI010000001-CAJRAI010000423. The assembly qDolPla1.1 is based on 55x PacBio data and 39x 10X Genomics Chromium data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding and improvement by the Aiden lab as part of a collaboration with DNA Zoo using 3D-DNA and Juicebox, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..423 /organism="Dolomedes plantarius" /mol_type="genomic DNA" /db_xref="taxon:257759" WGS CAJRAI010000001-CAJRAI010000423 // LOCUS CAJEUG020000000 197 rc DNA linear ROD 11-MAY-2021 DEFINITION Arvicola amphibius, whole genome shotgun sequencing project. ACCESSION CAJEUG000000000 VERSION CAJEUG000000000.2 DBLINK BioProject: PRJEB39550 BioSample: SAMEA994740 KEYWORDS WGS. SOURCE Arvicola amphibius (Eurasian water vole) ORGANISM Arvicola amphibius Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Cricetidae; Arvicolinae; Arvicola. REFERENCE 1 (bases 1 to 197) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (27-JUL-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 197) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (30-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On May 15, 2021 this sequence version replaced CAJEUG000000000.1. The Arvicola amphibius whole genome shotgun (WGS) project has the project accession CAJEUG000000000. This version of the project (02) has the accession number CAJEUG020000000, and consists of sequences CAJEUG020000001-CAJEUG020000197. The assembly mArvAmp1.2 is based on 45x PacBio data, 52x 10X Genomics Chromium data, BioNano data and 6x Dovetail Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Solve, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..197 /organism="Arvicola amphibius" /mol_type="genomic DNA" /db_xref="taxon:1047088" WGS CAJEUG020000001-CAJEUG020000197 // LOCUS CAJRBH010000000 181 rc DNA linear INV 11-MAY-2021 DEFINITION Nomada fabriciana, whole genome shotgun sequencing project. ACCESSION CAJRBH000000000 VERSION CAJRBH000000000.1 DBLINK BioProject: PRJEB44636 BioSample: SAMEA7520701 KEYWORDS WGS. SOURCE Nomada fabriciana ORGANISM Nomada fabriciana Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Nomadini; Nomada. REFERENCE 1 (bases 1 to 181) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Nomada fabriciana whole genome shotgun (WGS) project has the project accession CAJRBH000000000. This version of the project (01) has the accession number CAJRBH010000000, and consists of sequences CAJRBH010000001-CAJRBH010000181. The assembly iyNomFabr1.1 is based on 99x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..181 /organism="Nomada fabriciana" /mol_type="genomic DNA" /db_xref="taxon:601510" WGS CAJRBH010000001-CAJRBH010000181 // LOCUS CAJRAV010000000 84 rc DNA linear VRT 11-MAY-2021 DEFINITION Caprimulgus europaeus, whole genome shotgun sequencing project. ACCESSION CAJRAV000000000 VERSION CAJRAV000000000.1 DBLINK BioProject: PRJEB44540 BioSample: SAMEA7524394 KEYWORDS WGS. SOURCE Caprimulgus europaeus (Eurasian nightjar) ORGANISM Caprimulgus europaeus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Caprimulgimorphae; Caprimulgiformes; Caprimulgidae; Caprimulginae; Caprimulgus. REFERENCE 1 (bases 1 to 84) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (26-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Caprimulgus europaeus whole genome shotgun (WGS) project has the project accession CAJRAV000000000. This version of the project (01) has the accession number CAJRAV010000000, and consists of sequences CAJRAV010000001-CAJRAV010000084. The assembly bCapEur3.1 is based on 87x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Arrow polishing assisted by Merfin, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..84 /organism="Caprimulgus europaeus" /mol_type="genomic DNA" /db_xref="taxon:111811" WGS CAJRAV010000001-CAJRAV010000084 // LOCUS CAJRAZ010000000 14 rc DNA linear INV 11-MAY-2021 DEFINITION Coccinella septempunctata, whole genome shotgun sequencing project. ACCESSION CAJRAZ000000000 VERSION CAJRAZ000000000.1 DBLINK BioProject: PRJEB44629 BioSample: SAMEA7520205 KEYWORDS WGS. SOURCE Coccinella septempunctata (seven-spotted ladybird) ORGANISM Coccinella septempunctata Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Coccinellidae; Coccinellinae; Coccinellini; Coccinella. REFERENCE 1 (bases 1 to 14) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Coccinella septempunctata whole genome shotgun (WGS) project has the project accession CAJRAZ000000000. This version of the project (01) has the accession number CAJRAZ010000000, and consists of sequences CAJRAZ010000001-CAJRAZ010000014. The assembly icCocSept1.1 is based on 76x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..14 /organism="Coccinella septempunctata" /mol_type="genomic DNA" /db_xref="taxon:41139" WGS CAJRAZ010000001-CAJRAZ010000014 // LOCUS CAJRBB010000000 5 rc DNA linear INV 11-MAY-2021 DEFINITION Zeuzera pyrina, whole genome shotgun sequencing project. ACCESSION CAJRBB000000000 VERSION CAJRBB000000000.1 DBLINK BioProject: PRJEB44632 BioSample: SAMEA7701286 KEYWORDS WGS. SOURCE Zeuzera pyrina ORGANISM Zeuzera pyrina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Cossoidea; Cossidae; Zeuzerinae; Zeuzera. REFERENCE 1 (bases 1 to 5) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-APR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Zeuzera pyrina whole genome shotgun (WGS) project has the project accession CAJRBB000000000. This version of the project (01) has the accession number CAJRBB010000000, and consists of sequences CAJRBB010000001-CAJRBB010000005. The assembly ilZeuPyri1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..5 /organism="Zeuzera pyrina" /mol_type="genomic DNA" /db_xref="taxon:1101072" WGS CAJRBB010000001-CAJRBB010000005 // LOCUS CAJRAC010000000 12 rc DNA linear INV 11-MAY-2021 DEFINITION Hemaris fuciformis, whole genome shotgun sequencing project. ACCESSION CAJRAC000000000 VERSION CAJRAC000000000.1 DBLINK BioProject: PRJEB44424 BioSample: SAMEA5248724 KEYWORDS WGS. SOURCE Hemaris fuciformis ORGANISM Hemaris fuciformis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Sphingidae; Macroglossinae; Dilophonotini; Hemaris. REFERENCE 1 (bases 1 to 12) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (20-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT The Hemaris fuciformis whole genome shotgun (WGS) project has the project accession CAJRAC000000000. This version of the project (01) has the accession number CAJRAC010000000, and consists of sequences CAJRAC010000001-CAJRAC010000012. The assembly iHemFuc1.1 is based on 88x PacBio data, 88x 10X Genomics Chromium data, and BioNano data generated at the Wellcome Sanger Institute, and Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Solve, Hi-C based scaffolding and curation carried out at Baylor, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial genomes was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..12 /organism="Hemaris fuciformis" /mol_type="genomic DNA" /db_xref="taxon:987953" WGS CAJRAC010000001-CAJRAC010000012 // LOCUS CAJQTU010000000 142 rc DNA linear INV 07-MAY-2021 DEFINITION Desoria tigrina, whole genome shotgun sequencing project. ACCESSION CAJQTU000000000 VERSION CAJQTU000000000.1 DBLINK BioProject: PRJEB39696 BioSample: SAMEA7116352 Sequence Read Archive: ERR4407422 KEYWORDS WGS. SOURCE Desoria tigrina ORGANISM Desoria tigrina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Collembola; Entomobryomorpha; Isotomoidea; Isotomidae; Isotominae; Desoria. REFERENCE 1 (bases 1 to 142) AUTHORS Schneider,C. TITLE Direct Submission JOURNAL Submitted (29-APR-2021) LOEWE-TBG, Georg Voigt Str. 14-16, D-60325 Frankfurt am Main, Germany COMMENT The Desoria tigrina whole genome shotgun (WGS) project has the project accession CAJQTU000000000. This version of the project (01) has the accession number CAJQTU010000000, and consists of sequences CAJQTU010000001-CAJQTU010000142. Primary assembly assembled with Hifiasm from sequencing Data from a whole single specimen of Desoria tigrina. FEATURES Location/Qualifiers source 1..142 /organism="Desoria tigrina" /mol_type="genomic DNA" /isolation_source="Vegetal compost" /db_xref="taxon:370036" WGS CAJQTU010000001-CAJQTU010000142 // LOCUS CAJQTT010000000 79 rc DNA linear INV 07-MAY-2021 DEFINITION Sminthurides aquaticus, whole genome shotgun sequencing project. ACCESSION CAJQTT000000000 VERSION CAJQTT000000000.1 DBLINK BioProject: PRJEB39696 BioSample: SAMEA7116350 Sequence Read Archive: ERR4407379 KEYWORDS WGS. SOURCE Sminthurides aquaticus ORGANISM Sminthurides aquaticus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Collembola; Symphypleona; Sminthurididae; Sminthurides. REFERENCE 1 (bases 1 to 79) AUTHORS Schneider,C. TITLE Direct Submission JOURNAL Submitted (29-APR-2021) LOEWE-TBG, Georg Voigt Str. 14-16, D-60325 Frankfurt am Main, Germany COMMENT The Sminthurides aquaticus whole genome shotgun (WGS) project has the project accession CAJQTT000000000. This version of the project (01) has the accession number CAJQTT010000000, and consists of sequences CAJQTT010000001-CAJQTT010000079. Primary assembly assembled with Hifiasm from sequencing Data from a whole single specimen of Sminthurides aquaticus. FEATURES Location/Qualifiers source 1..79 /organism="Sminthurides aquaticus" /mol_type="genomic DNA" /isolation_source="On the surface of a pond" /db_xref="taxon:281415" WGS CAJQTT010000001-CAJQTT010000079 // LOCUS JABSTO010000000 10445 rc DNA linear MAM 05-MAY-2021 DEFINITION Giraffa camelopardalis antiquorum isolate PLA01, whole genome shotgun sequencing project. ACCESSION JABSTO000000000 VERSION JABSTO000000000.1 DBLINK BioProject: PRJNA635165 BioSample: SAMN15027847 KEYWORDS WGS. SOURCE Giraffa camelopardalis antiquorum (Kordofan giraffe) ORGANISM Giraffa camelopardalis antiquorum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Giraffidae; Giraffa. REFERENCE 1 (bases 1 to 10445) AUTHORS Coimbra,R.T.F., Winter,S., Kumar,V., Koepfli,K.-P., Gooley,R.M., Dobrynin,P., Fennessy,J. and Janke,A. TITLE Whole-genome analysis of giraffe supports four distinct species JOURNAL Curr Biol (2021) In press REFERENCE 2 (bases 1 to 10445) AUTHORS Coimbra,R.T.F. and Winter,S. TITLE Direct Submission JOURNAL Submitted (30-MAY-2020) Biodiversity and Climate Research Centre, Senckenberg Nature Research Society, Senckenberganlage 25, Frankfurt am Main, Hesse 60325, Germany COMMENT The Giraffa camelopardalis antiquorum whole genome shotgun (WGS) project has the project accession JABSTO000000000. This version of the project (01) has the accession number JABSTO010000000, and consists of sequences JABSTO010000001-JABSTO010010445. ##Genome-Assembly-Data-START## Assembly Method :: Supernova v. 2.1.1 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 30.0x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..10445 /organism="Giraffa camelopardalis antiquorum" /mol_type="genomic DNA" /isolate="PLA01" /sub_species="antiquorum" /db_xref="taxon:439324" /sex="male" /tissue_type="blood" /dev_stage="adult" WGS JABSTO010000001-JABSTO010010445 // LOCUS CAIGJR020000000 1086 rc DNA linear VRT 01-MAY-2021 DEFINITION Erithacus rubecula, whole genome shotgun sequencing project. ACCESSION CAIGJR000000000 VERSION CAIGJR000000000.2 DBLINK BioProject: PRJEB38658 BioSample: SAMEA4760689 KEYWORDS WGS. SOURCE Erithacus rubecula (European robin) ORGANISM Erithacus rubecula Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Turdidae; Erithacus. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (03-JUN-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 1086) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (03-MAR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On May 1, 2021 this sequence version replaced CAIGJR000000000.1. The Erithacus rubecula whole genome shotgun (WGS) project has the project accession CAIGJR000000000. This version of the project (02) has the accession number CAIGJR020000000, and consists of sequences CAIGJR020000001-CAIGJR020001086. The assembly bEriRub2.2 is based on 41x PacBio data, 22x 10X Genomics Chromium data, and 42x Dovetail Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1086 /organism="Erithacus rubecula" /mol_type="genomic DNA" /db_xref="taxon:37610" WGS CAIGJR020000001-CAIGJR020001086 // LOCUS JAALXR020000000 1217 rc DNA linear PRI 28-APR-2021 DEFINITION Callithrix jacchus isolate mCalJac1, whole genome shotgun sequencing project. ACCESSION JAALXR000000000 VERSION JAALXR000000000.2 DBLINK BioProject: PRJNA558087 BioSample: SAMN12368443 KEYWORDS WGS. SOURCE Callithrix jacchus (white-tufted-ear marmoset) ORGANISM Callithrix jacchus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Platyrrhini; Cebidae; Callitrichinae; Callithrix; Callithrix. REFERENCE 1 (bases 1 to 1217) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Callithrix jacchus (common marmoset) genome, mCalJac1, paternal haplotype, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 1217) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Direct Submission JOURNAL Submitted (25-FEB-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 1217) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Direct Submission JOURNAL Submitted (25-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 27, 2021 this sequence version replaced JAALXR000000000.1. The Callithrix jacchus whole genome shotgun (WGS) project has the project accession JAALXR000000000. This version of the project (02) has the accession number JAALXR020000000, and consists of sequences JAALXR020000001-JAALXR020001217. ##Genome-Assembly-Data-START## Assembly Date :: 25-APR-2021 Assembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. smrtlink_6.0.0.47841; Longranger Align v. 2.2.2; Freebayes v. 1.3.1; gEVAL manual curation v. 2019-12-11; Zhang manual curation v. 2021-04-25; VGP assembly pipeline v. 1.6 Assembly Name :: mCalJac1.2.pat Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 63.44x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1217 /organism="Callithrix jacchus" /mol_type="genomic DNA" /isolate="mCalJac1" /db_xref="taxon:9483" /sex="male" /tissue_type="muscle" /dev_stage="juvenile" /country="USA: New York" /lat_lon="40.762676 N 73.955541 W" /collection_date="2018-06-12" /collected_by="Stephanie Marcus and Margaret Fabiszak" WGS JAALXR020000001-JAALXR020001217 WGS_SCAFLD CM021882-CM021904 // LOCUS JAALXP020000000 1234 rc DNA linear PRI 28-APR-2021 DEFINITION Callithrix jacchus isolate mCalJac1, whole genome shotgun sequencing project. ACCESSION JAALXP000000000 VERSION JAALXP000000000.2 DBLINK BioProject: PRJNA597600 BioSample: SAMN12368443 KEYWORDS WGS. SOURCE Callithrix jacchus (white-tufted-ear marmoset) ORGANISM Callithrix jacchus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Platyrrhini; Cebidae; Callitrichinae; Callithrix; Callithrix. REFERENCE 1 (bases 1 to 1234) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Callithrix jacchus (common marmoset) genome, mCalJac1, paternal haplotype + X, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 1234) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Direct Submission JOURNAL Submitted (25-FEB-2020) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 1234) AUTHORS Marcus,S., Zhou,Y., Formenti,G., Mountcastle,J., Haase,B., Balacco,J., Fabiszak,M., Rhie,A., Phillippy,A., Wood,J., Chow,W., Yang,C., Howe,K., Fedrigo,O., Freiwald,W., Jarvis,E.D. and Zhang,G. TITLE Direct Submission JOURNAL Submitted (25-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Apr 27, 2021 this sequence version replaced JAALXP000000000.1. The Callithrix jacchus whole genome shotgun (WGS) project has the project accession JAALXP000000000. This version of the project (02) has the accession number JAALXP020000000, and consists of sequences JAALXP020000001-JAALXP020001234. ##Genome-Assembly-Data-START## Assembly Date :: 25-APR-2021 Assembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. smrtlink_6.0.0.47841; Longranger Align v. 2.2.2; Freebayes v. 1.3.1; gEVAL manual curation v. 2019-12-11; Zhang manual curation v. 2021-04-25; VGP assembly pipeline v. 1.6 Assembly Name :: mCalJa1.2.pat.X Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 63.44x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1234 /organism="Callithrix jacchus" /mol_type="genomic DNA" /isolate="mCalJac1" /db_xref="taxon:9483" /sex="male" /tissue_type="muscle" /dev_stage="juvenile" /country="USA: New York" /lat_lon="40.762676 N 73.955541 W" /collection_date="2018-06-12" /collected_by="Stephanie Marcus and Margaret Fabiszak" WGS JAALXP020000001-JAALXP020001234 WGS_SCAFLD CM021915-CM021938 WGS_SCAFLD CM021961 // LOCUS CAAJIE020000000 1400 rc DNA linear VRT 23-APR-2021 DEFINITION Salmo trutta, whole genome shotgun sequencing project. ACCESSION CAAJIE000000000 VERSION CAAJIE000000000.2 DBLINK BioProject: PRJEB32115 BioSample: SAMEA994732 KEYWORDS WGS. SOURCE Salmo trutta (river trout) ORGANISM Salmo trutta Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (10-APR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 1400) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CAAJIE000000000.1. The Salmo trutta whole genome shotgun (WGS) project has the project accession CAAJIE000000000. This version of the project (02) has the accession number CAAJIE020000000, and consists of sequences CAAJIE020000001-CAAJIE020001400. The assembly fSalTru1.2 is based on 68x PacBio data and 70x coverage 10X Genomics Chromium data generated at the Wellcome Sanger Institute, as well as BioNano data generated at the Rockefeller University Vertebrate Genome Laboratory and 28x coverage Hi-C data generated by Arima Genomics. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named on the following basis: first they were assigned as metacentric versus acrocentric based on a Salmo trutta linkage map and synteny with the Salmo salar assembly GCA_000233375.4; numbers 1 to 11 are metacentric, numbers 12 to 40 are acrocentric, and within each of those two categories they are named in order of size. FEATURES Location/Qualifiers source 1..1400 /organism="Salmo trutta" /mol_type="genomic DNA" /db_xref="taxon:8032" WGS CAAJIE020000001-CAAJIE020001400 // LOCUS CAAJIB020000000 1310 rc DNA linear VRT 23-APR-2021 DEFINITION Rhinatrema bivittatum, whole genome shotgun sequencing project. ACCESSION CAAJIB000000000 VERSION CAAJIB000000000.2 DBLINK BioProject: PRJEB32111 BioSample: SAMEA104387956 KEYWORDS WGS. SOURCE Rhinatrema bivittatum (two-lined caecilian) ORGANISM Rhinatrema bivittatum Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Gymnophiona; Rhinatrematidae; Rhinatrema. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (10-APR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 1310) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (12-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CAAJIB000000000.1. The Rhinatrema bivittatum whole genome shotgun (WGS) project has the project accession CAAJIB000000000. This version of the project (02) has the accession number CAAJIB020000000, and consists of sequences CAAJIB020000001-CAAJIB020001310. The assembly aRhiBiv1.2 is based on 43x PacBio data and 41x coverage 10X Genomics Chromium data generated at the Wellcome Sanger Institute, BioNano data generated by BioNano Genomics, and 39x coverage Hi-C data generated at the Wellcome Sanger Institute using a library created by Arima Genomics. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1310 /organism="Rhinatrema bivittatum" /mol_type="genomic DNA" /db_xref="taxon:194408" WGS CAAJIB020000001-CAAJIB020001310 // LOCUS CABFKK020000000 1066 rc DNA linear VRT 23-APR-2021 DEFINITION Microcaecilia unicolor, whole genome shotgun sequencing project. ACCESSION CABFKK000000000 VERSION CABFKK000000000.2 DBLINK BioProject: PRJEB32737 BioSample: SAMEA104387962 KEYWORDS WGS. SOURCE Microcaecilia unicolor ORGANISM Microcaecilia unicolor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Gymnophiona; Siphonopidae; Microcaecilia. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (28-MAY-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 1066) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (12-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CABFKK000000000.1. The Microcaecilia unicolor whole genome shotgun (WGS) project has the project accession CABFKK000000000. This version of the project (02) has the accession number CABFKK020000000, and consists of sequences CABFKK020000001-CABFKK020001066. The assembly aMicUni1.2 is based on 53x PacBio data, 52x coverage 10X Genomics Chromium data, BioNano data and 25x coverage Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1066 /organism="Microcaecilia unicolor" /mol_type="genomic DNA" /db_xref="taxon:1415580" WGS CABFKK020000001-CABFKK020001066 // LOCUS OOHQ03000000 98 rc DNA linear VRT 23-APR-2021 DEFINITION Mastacembelus armatus, whole genome shotgun sequencing project. ACCESSION OOHQ00000000 VERSION OOHQ00000000.3 DBLINK BioProject: PRJEB25769 BioSample: SAMEA104026378 KEYWORDS WGS. SOURCE Mastacembelus armatus (zig-zag eel) ORGANISM Mastacembelus armatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Anabantaria; Synbranchiformes; Mastacembelidae; Mastacembelus. REFERENCE 1 AUTHORS Datahose. TITLE Direct Submission JOURNAL Submitted (28-MAR-2018) SC, Wellcome Trust Sanger Institute, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 98) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced OOHQ00000000.2. The Mastacembelus armatus whole genome shotgun (WGS) project has the project accession OOHQ00000000. This version of the project (03) has the accession number OOHQ03000000, and consists of sequences OOHQ03000001-OOHQ03000098. The assembly fMasArm1.3 is based on 52x PacBio Sequel data, 99x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute, as well as two-enzyme BioNano Saphyr data generated at the Rockefeller University Vertebrate Genome Laboratory and 245x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip and the primary contigs extended by merging with a miniasm assembly. The contigs were then scaffolded using the 10X data with scaff10x, and using synteny with Lates calcarifer (Asian seabass). After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the 10X Illumina data and freebayes. Finally, the assembly was further manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano and Arima Hi-C data. This was the fMasArm1.1 assembly. A updated fMasArm1.2 assembly has been further curated using the Hi-C data to separate out haplotigs, identify further breaks and joins and produce chromosomal-level scaffolds. The further updated fMasArm1.3 assembly includes a mitochondrial assembly produced at The Rockefeller University using mitoVGP. Chromosomes have been named by synteny to medaka. FEATURES Location/Qualifiers source 1..98 /organism="Mastacembelus armatus" /mol_type="genomic DNA" /db_xref="taxon:205130" WGS OOHQ03000001-OOHQ03000098 // LOCUS CAAHFC020000000 151 rc DNA linear VRT 23-APR-2021 DEFINITION Sparus aurata, whole genome shotgun sequencing project. ACCESSION CAAHFC000000000 VERSION CAAHFC000000000.2 DBLINK BioProject: PRJEB31901 BioSample: SAMEA104384835 KEYWORDS WGS. SOURCE Sparus aurata (gilthead seabream) ORGANISM Sparus aurata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Spariformes; Sparidae; Sparus. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (28-MAR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 151) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CAAHFC000000000.1. The Sparus aurata whole genome shotgun (WGS) project has the project accession CAAHFC000000000. This version of the project (02) has the accession number CAAHFC020000000, and consists of sequences CAAHFC020000001-CAAHFC020000151. The assembly fSpaAur1.2 is based on 56x PacBio Sequel data, 62x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute, as well as 71x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the raw data. Chromosomes are named according to synteny with the GCA_003309015.1 assembly of Sparus aurata. FEATURES Location/Qualifiers source 1..151 /organism="Sparus aurata" /mol_type="genomic DNA" /db_xref="taxon:8175" WGS CAAHFC020000001-CAAHFC020000151 // LOCUS CABPRQ020000000 144 rc DNA linear VRT 23-APR-2021 DEFINITION Geotrypetes seraphini, whole genome shotgun sequencing project. ACCESSION CABPRQ000000000 VERSION CABPRQ000000000.2 DBLINK BioProject: PRJEB33992 BioSample: SAMEA104387963 KEYWORDS WGS. SOURCE Geotrypetes seraphini ORGANISM Geotrypetes seraphini Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Gymnophiona; Geotrypetes. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-AUG-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 144) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (12-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CABPRQ000000000.1. The Geotrypetes seraphini whole genome shotgun (WGS) project has the project accession CABPRQ000000000. This version of the project (02) has the accession number CABPRQ020000000, and consists of sequences CABPRQ020000001-CABPRQ020000144. The assembly aGeoSer1.2 is based on 67x PacBio data, 28x 10X Genomics Chromium data, BioNano data and 20x Dovetail Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..144 /organism="Geotrypetes seraphini" /mol_type="genomic DNA" /db_xref="taxon:260995" WGS CABPRQ020000001-CABPRQ020000144 // LOCUS CAAHFO020000000 13 rc DNA linear VRT 23-APR-2021 DEFINITION Echeneis naucrates, whole genome shotgun sequencing project. ACCESSION CAAHFO000000000 VERSION CAAHFO000000000.2 DBLINK BioProject: PRJEB31992 BioSample: SAMEA4966390 KEYWORDS WGS. SOURCE Echeneis naucrates (live sharksucker) ORGANISM Echeneis naucrates Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Carangaria; Carangiformes; Echeneidae; Echeneis. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (02-APR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 13) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CAAHFO000000000.1. The Echeneis naucrates whole genome shotgun (WGS) project has the project accession CAAHFO000000000. This version of the project (02) has the accession number CAAHFO020000000, and consists of sequences CAAHFO020000001-CAAHFO020000013. The assembly fEcheNa1.2 is based on 62x PacBio data, 100x coverage 10X Genomics Chromium data, BioNano data and 112x coverage Dovetail Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny to medaka. FEATURES Location/Qualifiers source 1..13 /organism="Echeneis naucrates" /mol_type="genomic DNA" /db_xref="taxon:173247" WGS CAAHFO020000001-CAAHFO020000013 // LOCUS OOHO03000000 27 rc DNA linear VRT 23-APR-2021 DEFINITION Anabas testudineus, whole genome shotgun sequencing project. ACCESSION OOHO00000000 VERSION OOHO00000000.3 DBLINK BioProject: PRJEB25768 BioSample: SAMEA104026376 KEYWORDS WGS. SOURCE Anabas testudineus (climbing perch) ORGANISM Anabas testudineus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Anabantaria; Anabantiformes; Anabantoidei; Anabantidae; Anabas. REFERENCE 1 AUTHORS Datahose. TITLE Direct Submission JOURNAL Submitted (28-MAR-2018) SC, Wellcome Trust Sanger Institute, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 27) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (12-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced OOHO00000000.2. The Anabas testudineus whole genome shotgun (WGS) project has the project accession OOHO00000000. This version of the project (03) has the accession number OOHO03000000, and consists of sequences OOHO03000001-OOHO03000027. The assembly fAnaTes1.3 is based on 68x PacBio Sequel data, 114x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory and 170x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip. The primary contigs were then scaffolded using the 10X data with scaff10x and mis-joins broken using break10x. After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the 10X Illumina data and freebayes. Finally, the assembly was further manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano data and Arima Hi-C data. This was the initial fAnaTes1.1 assembly. An updated fAnaTes1.2 assembly has been further curated to removed duplicate haplotypes using purge_haplotigs and using the Hi-C data to identify further breaks and joins and produce chromosomal-level scaffolds. fAnaTes1.3 includes a mitochondrial assembly produced at The Rockefeller University using mitoVGP. Chromosomes have been named by synteny to medaka. FEATURES Location/Qualifiers source 1..27 /organism="Anabas testudineus" /mol_type="genomic DNA" /db_xref="taxon:64144" WGS OOHO03000001-OOHO03000027 // LOCUS CAAJGN030000000 105 rc DNA linear VRT 23-APR-2021 DEFINITION Takifugu rubripes, whole genome shotgun sequencing project. ACCESSION CAAJGN000000000 VERSION CAAJGN000000000.3 DBLINK BioProject: PRJEB31988 BioSample: SAMEA104384834 KEYWORDS WGS. SOURCE Takifugu rubripes (torafugu) ORGANISM Takifugu rubripes Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Takifugu. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (05-APR-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 105) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (13-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 24, 2021 this sequence version replaced CAAJGN000000000.2. The Takifugu rubripes whole genome shotgun (WGS) project has the project accession CAAJGN000000000. This version of the project (03) has the accession number CAAJGN030000000, and consists of sequences CAAJGN030000001-CAAJGN030000105. The assembly fTakRub1.3 is based on 83x PacBio Sequel data, 70x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory and 51x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further with BioNano hybrid scaffolding and scaffolded further still using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano and Hi-C data. Chromosome-scale scaffolds are named by synteny to the GCA_000180615.2 assembly of Takifugu rubripes. FEATURES Location/Qualifiers source 1..105 /organism="Takifugu rubripes" /mol_type="genomic DNA" /db_xref="taxon:31033" WGS CAAJGN030000001-CAAJGN030000105 // LOCUS JAGIYW010000000 2125 rc DNA linear VRT 15-APR-2021 DEFINITION Chelmon rostratus isolate fCheRos1, whole genome shotgun sequencing project. ACCESSION JAGIYW000000000 VERSION JAGIYW000000000.1 DBLINK BioProject: PRJNA561970 BioSample: SAMN12623620 KEYWORDS WGS. SOURCE Chelmon rostratus (copperband butterflyfish) ORGANISM Chelmon rostratus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Chaetodontiformes; Chaetodontidae; Chelmon. REFERENCE 1 (bases 1 to 2125) AUTHORS Myers,G., Venkatesh,B., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Formenti,G., Bista,I., Jarvis,R., Fedrigo,O. and Jarvis,E.D. TITLE Chelmon rostratus (copperband butterflyfish) genome, fCheRos1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 2125) AUTHORS Myers,G., Venkatesh,B., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Formenti,G., Bista,I., Jarvis,R., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Chelmon rostratus whole genome shotgun (WGS) project has the project accession JAGIYW000000000. This version of the project (01) has the accession number JAGIYW010000000, and consists of sequences JAGIYW010000001-JAGIYW010002125. ##Genome-Assembly-Data-START## Assembly Date :: 24-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-24; VGP assembly pipeline v. 1.5 Assembly Name :: fCheRos1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2125 /organism="Chelmon rostratus" /mol_type="genomic DNA" /isolate="fCheRos1" /db_xref="taxon:109905" /tissue_type="liver" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-06-20" /collected_by="Byrappa Venkatesh" WGS JAGIYW010000001-JAGIYW010002125 // LOCUS JAGIYS010000000 2393 rc DNA linear VRT 15-APR-2021 DEFINITION Toxotes jaculatrix isolate fToxJac2, whole genome shotgun sequencing project. ACCESSION JAGIYS000000000 VERSION JAGIYS000000000.1 DBLINK BioProject: PRJNA717045 BioSample: SAMN18445299 KEYWORDS WGS. SOURCE Toxotes jaculatrix (banded archerfish) ORGANISM Toxotes jaculatrix Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Carangaria; Carangaria incertae sedis; Toxotidae; Toxotes. REFERENCE 1 (bases 1 to 2393) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Sims,Y., Howe,K., Meyers,A., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Toxotes jaculatrix (banded archerfish) genome, fToxJac2, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 2393) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Sims,Y., Howe,K., Meyers,A., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Toxotes jaculatrix whole genome shotgun (WGS) project has the project accession JAGIYS000000000. This version of the project (01) has the accession number JAGIYS010000000, and consists of sequences JAGIYS010000001-JAGIYS010002393. ##Genome-Assembly-Data-START## Assembly Date :: 05-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; Assembly Polish v. SMRTLink7.0.1; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-05; VGP assembly pipeline v. 1.6 Assembly Name :: fToxJac2.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..2393 /organism="Toxotes jaculatrix" /mol_type="genomic DNA" /isolate="fToxJac2" /db_xref="taxon:941984" /tissue_type="liver, intestine, and heart used for different sequencing technologies" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2019-10-29" /collected_by="Byrappa Venkatesh" WGS JAGIYS010000001-JAGIYS010002393 // LOCUS JAGIYU010000000 1004 rc DNA linear VRT 15-APR-2021 DEFINITION Cuculus canorus isolate bCucCan1, whole genome shotgun sequencing project. ACCESSION JAGIYU000000000 VERSION JAGIYU000000000.1 DBLINK BioProject: PRJNA562016 BioSample: SAMN12629508 KEYWORDS WGS. SOURCE Cuculus canorus (common cuckoo) ORGANISM Cuculus canorus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Cuculiformes; Cuculidae; Cuculus. REFERENCE 1 (bases 1 to 1004) AUTHORS Wolf,J., Merondon,J., Haase,B., Formenti,G., Prochazka,P., Sulc,M., Tracey,A., Sims,Y., Howe,K., Mountcastle,J., Balacco,J., Fedrigo,O. and Jarvis,E.D. TITLE Cuculus canorus (Common cuckoo) genome, bCucCan1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1004) AUTHORS Wolf,J., Merondon,J., Haase,B., Formenti,G., Prochazka,P., Sulc,M., Tracey,A., Sims,Y., Howe,K., Mountcastle,J., Balacco,J., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Cuculus canorus whole genome shotgun (WGS) project has the project accession JAGIYU000000000. This version of the project (01) has the accession number JAGIYU010000000, and consists of sequences JAGIYU010000001-JAGIYU010001004. ##Genome-Assembly-Data-START## Assembly Date :: 30-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-30; VGP assembly pipeline v. 1.5 Assembly Name :: bCucCan1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 64.31x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1004 /organism="Cuculus canorus" /mol_type="genomic DNA" /isolate="bCucCan1" /db_xref="taxon:55661" /sex="female" /tissue_type="blood" /dev_stage="adult" /country="Czech Republic: Hodonin" /lat_lon="48.8557750 N 17.0677347 E" /collection_date="2018-05-08" /collected_by="Michal Sulc" WGS JAGIYU010000001-JAGIYU010001004 // LOCUS JAGIYV010000000 29 rc DNA linear VRT 15-APR-2021 DEFINITION Chelmon rostratus isolate fCheRos1, whole genome shotgun sequencing project. ACCESSION JAGIYV000000000 VERSION JAGIYV000000000.1 DBLINK BioProject: PRJNA561969 BioSample: SAMN12623620 KEYWORDS WGS. SOURCE Chelmon rostratus (copperband butterflyfish) ORGANISM Chelmon rostratus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Eupercaria; Chaetodontiformes; Chaetodontidae; Chelmon. REFERENCE 1 (bases 1 to 29) AUTHORS Myers,G., Venkatesh,B., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Formenti,G., Bista,I., Durbin,R., Fedrigo,O. and Jarvis,E.D. TITLE Chelmon rostratus (copperband butterflyfish) genome, fCheRos1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 29) AUTHORS Myers,G., Venkatesh,B., Pippel,M., Winkler,S., Tracey,A., Chow,W., Howe,K., Formenti,G., Bista,I., Durbin,R., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Chelmon rostratus whole genome shotgun (WGS) project has the project accession JAGIYV000000000. This version of the project (01) has the accession number JAGIYV010000000, and consists of sequences JAGIYV010000001-JAGIYV010000029. ##Genome-Assembly-Data-START## Assembly Date :: 24-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-24; VGP assembly pipeline v. 1.5 Assembly Name :: fCheRos1.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..29 /organism="Chelmon rostratus" /mol_type="genomic DNA" /isolate="fCheRos1" /db_xref="taxon:109905" /tissue_type="liver" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-06-20" /collected_by="Byrappa Venkatesh" WGS JAGIYV010000001-JAGIYV010000029 WGS_SCAFLD CM030613-CM030636 WGS_SCAFLD CM030678 // LOCUS JAGIYT010000000 151 rc DNA linear VRT 15-APR-2021 DEFINITION Cuculus canorus isolate bCucCan1, whole genome shotgun sequencing project. ACCESSION JAGIYT000000000 VERSION JAGIYT000000000.1 DBLINK BioProject: PRJNA562015 BioSample: SAMN12629508 KEYWORDS WGS. SOURCE Cuculus canorus (common cuckoo) ORGANISM Cuculus canorus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Cuculiformes; Cuculidae; Cuculus. REFERENCE 1 (bases 1 to 151) AUTHORS Wolf,J., Merondon,J., Haase,B., Formenti,G., Prochazka,P., Sulc,M., Tracey,A., Sims,Y., Howe,K., Mountcastle,J., Balacco,J., Fedrigo,O. and Jarvis,E.D. TITLE Cuculus canorus (Common cuckoo) genome, bCucCan1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 151) AUTHORS Wolf,J., Merondon,J., Haase,B., Formenti,G., Prochazka,P., Sulc,M., Tracey,A., Sims,Y., Howe,K., Mountcastle,J., Balacco,J., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Cuculus canorus whole genome shotgun (WGS) project has the project accession JAGIYT000000000. This version of the project (01) has the accession number JAGIYT010000000, and consists of sequences JAGIYT010000001-JAGIYT010000151. ##Genome-Assembly-Data-START## Assembly Date :: 30-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-30; VGP assembly pipeline v. 1.5 Assembly Name :: bCucCan1.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 64.31x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..151 /organism="Cuculus canorus" /mol_type="genomic DNA" /isolate="bCucCan1" /db_xref="taxon:55661" /sex="female" /tissue_type="blood" /dev_stage="adult" /country="Czech Republic: Hodonin" /lat_lon="48.8557750 N 17.0677347 E" /collection_date="2018-05-08" /collected_by="Michal Sulc" WGS JAGIYT010000001-JAGIYT010000151 WGS_SCAFLD CM030637-CM030677 WGS_SCAFLD CM030679 // LOCUS JAGIYR010000000 96 rc DNA linear VRT 15-APR-2021 DEFINITION Toxotes jaculatrix isolate fToxJac2, whole genome shotgun sequencing project. ACCESSION JAGIYR000000000 VERSION JAGIYR000000000.1 DBLINK BioProject: PRJNA717046 BioSample: SAMN18445299 KEYWORDS WGS. SOURCE Toxotes jaculatrix (banded archerfish) ORGANISM Toxotes jaculatrix Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Carangaria; Carangaria incertae sedis; Toxotidae; Toxotes. REFERENCE 1 (bases 1 to 96) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Sims,Y., Howe,K., Meyers,A., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Toxotes jaculatrix (banded archerfish) genome, fToxJac2, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 96) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Sims,Y., Howe,K., Meyers,A., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (01-APR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Toxotes jaculatrix whole genome shotgun (WGS) project has the project accession JAGIYR000000000. This version of the project (01) has the accession number JAGIYR010000000, and consists of sequences JAGIYR010000001-JAGIYR010000096. ##Genome-Assembly-Data-START## Assembly Date :: 05-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; Assembly Polish v. SMRTLink7.0.1; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-05; VGP assembly pipeline v. 1.6 Assembly Name :: fToxJac2.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..96 /organism="Toxotes jaculatrix" /mol_type="genomic DNA" /isolate="fToxJac2" /db_xref="taxon:941984" /tissue_type="liver, intestine, and heart used for different sequencing technologies" /dev_stage="adult" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2019-10-29" /collected_by="Byrappa Venkatesh" WGS JAGIYR010000001-JAGIYR010000096 WGS_SCAFLD CM030680-CM030703 // LOCUS CABFKB020000000 3334 rc DNA linear VRT 14-APR-2021 DEFINITION Streptopelia turtur, whole genome shotgun sequencing project. ACCESSION CABFKB000000000 VERSION CABFKB000000000.2 DBLINK BioProject: PRJEB32725 BioSample: SAMEA994735 KEYWORDS WGS. SOURCE Streptopelia turtur ORGANISM Streptopelia turtur Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Streptopelia. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (24-MAY-2019) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 3334) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (06-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 15, 2021 this sequence version replaced CABFKB000000000.1. The Streptopelia turtur whole genome shotgun (WGS) project has the project accession CABFKB000000000. This version of the project (02) has the accession number CABFKB020000000, and consists of sequences CABFKB020000001-CABFKB020003334. The assembly bStrTur1.2 is based on 44x PacBio data, 62x coverage 10X Genomics Chromium data, and BioNano data generated at the Wellcome Sanger Institute, and 106x coverage Hi-C data generated by Arima Genomics. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny to Gallus gallus. FEATURES Location/Qualifiers source 1..3334 /organism="Streptopelia turtur" /mol_type="genomic DNA" /db_xref="taxon:177155" WGS CABFKB020000001-CABFKB020003334 // LOCUS CAJQFE010000000 421 rc DNA linear INV 14-APR-2021 DEFINITION Leptidea sinapis, whole genome shotgun sequencing project. ACCESSION CAJQFE000000000 VERSION CAJQFE000000000.1 DBLINK BioProject: PRJEB43999 BioSample: SAMEA7523467 KEYWORDS WGS. SOURCE Leptidea sinapis ORGANISM Leptidea sinapis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Dismorphiinae; Leptidea. REFERENCE 1 (bases 1 to 421) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Leptidea sinapis whole genome shotgun (WGS) project has the project accession CAJQFE000000000. This version of the project (01) has the accession number CAJQFE010000000, and consists of sequences CAJQFE010000001-CAJQFE010000421. The assembly ilLepSina1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..421 /organism="Leptidea sinapis" /mol_type="genomic DNA" /db_xref="taxon:189913" WGS CAJQFE010000001-CAJQFE010000421 // LOCUS CAJQFM010000000 1472 rc DNA linear INV 14-APR-2021 DEFINITION Glaucopsyche alexis, whole genome shotgun sequencing project. ACCESSION CAJQFM000000000 VERSION CAJQFM000000000.1 DBLINK BioProject: PRJEB43993 BioSample: SAMEA7524616 KEYWORDS WGS. SOURCE Glaucopsyche alexis (green-underside blue) ORGANISM Glaucopsyche alexis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Lycaenidae; Polyommatinae; Glaucopsyche. REFERENCE 1 (bases 1 to 1472) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Glaucopsyche alexis whole genome shotgun (WGS) project has the project accession CAJQFM000000000. This version of the project (01) has the accession number CAJQFM010000000, and consists of sequences CAJQFM010000001-CAJQFM010001472. The assembly ilGlaAlex1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1472 /organism="Glaucopsyche alexis" /mol_type="genomic DNA" /db_xref="taxon:203781" WGS CAJQFM010000001-CAJQFM010001472 // LOCUS CAJQFX010000000 1048 rc DNA linear INV 14-APR-2021 DEFINITION Ochropleura plecta, whole genome shotgun sequencing project. ACCESSION CAJQFX000000000 VERSION CAJQFX000000000.1 DBLINK BioProject: PRJEB44050 BioSample: SAMEA7520524 KEYWORDS WGS. SOURCE Ochropleura plecta ORGANISM Ochropleura plecta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Ochropleura. REFERENCE 1 (bases 1 to 1048) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ochropleura plecta whole genome shotgun (WGS) project has the project accession CAJQFX000000000. This version of the project (01) has the accession number CAJQFX010000000, and consists of sequences CAJQFX010000001-CAJQFX010001048. The assembly ilOchPlec1.1 is based on 46x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1048 /organism="Ochropleura plecta" /mol_type="genomic DNA" /db_xref="taxon:320037" WGS CAJQFX010000001-CAJQFX010001048 // LOCUS CAJQGC010000000 486 rc DNA linear INV 14-APR-2021 DEFINITION Schrankia costaestrigalis, whole genome shotgun sequencing project. ACCESSION CAJQGC000000000 VERSION CAJQGC000000000.1 DBLINK BioProject: PRJEB44054 BioSample: SAMEA7520193 KEYWORDS WGS. SOURCE Schrankia costaestrigalis (pinion-streaked snout moth) ORGANISM Schrankia costaestrigalis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Hypeninae; Schrankia. REFERENCE 1 (bases 1 to 486) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Schrankia costaestrigalis whole genome shotgun (WGS) project has the project accession CAJQGC000000000. This version of the project (01) has the accession number CAJQGC010000000, and consists of sequences CAJQGC010000001-CAJQGC010000486. The assembly ilSchCost1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..486 /organism="Schrankia costaestrigalis" /mol_type="genomic DNA" /db_xref="taxon:411963" WGS CAJQGC010000001-CAJQGC010000486 // LOCUS CAJQFW010000000 432 rc DNA linear INV 14-APR-2021 DEFINITION Chrysoperla carnea, whole genome shotgun sequencing project. ACCESSION CAJQFW000000000 VERSION CAJQFW000000000.1 DBLINK BioProject: PRJEB44057 BioSample: SAMEA7520372 KEYWORDS WGS. SOURCE Chrysoperla carnea ORGANISM Chrysoperla carnea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Neuroptera; Hemerobiiformia; Chrysopidae; Chrysopinae; Chrysoperla. REFERENCE 1 (bases 1 to 432) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysoperla carnea whole genome shotgun (WGS) project has the project accession CAJQFW000000000. This version of the project (01) has the accession number CAJQFW010000000, and consists of sequences CAJQFW010000001-CAJQFW010000432. The assembly inChrCarn1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..432 /organism="Chrysoperla carnea" /mol_type="genomic DNA" /db_xref="taxon:189513" WGS CAJQFW010000001-CAJQFW010000432 // LOCUS CAJQFH010000000 1029 rc DNA linear INV 14-APR-2021 DEFINITION Erannis defoliaria, whole genome shotgun sequencing project. ACCESSION CAJQFH000000000 VERSION CAJQFH000000000.1 DBLINK BioProject: PRJEB43989 BioSample: SAMEA7520367 KEYWORDS WGS. SOURCE Erannis defoliaria ORGANISM Erannis defoliaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Erannis. REFERENCE 1 (bases 1 to 1029) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Erannis defoliaria whole genome shotgun (WGS) project has the project accession CAJQFH000000000. This version of the project (01) has the accession number CAJQFH010000000, and consists of sequences CAJQFH010000001-CAJQFH010001029. The assembly ilEraDefo1.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1029 /organism="Erannis defoliaria" /mol_type="genomic DNA" /db_xref="taxon:104474" WGS CAJQFH010000001-CAJQFH010001029 // LOCUS CAJQFY010000000 1277 rc DNA linear INV 14-APR-2021 DEFINITION Clostera curtula, whole genome shotgun sequencing project. ACCESSION CAJQFY000000000 VERSION CAJQFY000000000.1 DBLINK BioProject: PRJEB43987 BioSample: SAMEA7520526 KEYWORDS WGS. SOURCE Clostera curtula ORGANISM Clostera curtula Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Pygaerinae; Clostera. REFERENCE 1 (bases 1 to 1277) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Clostera curtula whole genome shotgun (WGS) project has the project accession CAJQFY000000000. This version of the project (01) has the accession number CAJQFY010000000, and consists of sequences CAJQFY010000001-CAJQFY010001277. The assembly ilCloCurt1.1 is based on 24x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1277 /organism="Clostera curtula" /mol_type="genomic DNA" /db_xref="taxon:987902" WGS CAJQFY010000001-CAJQFY010001277 // LOCUS CAJQEY010000000 451 rc DNA linear INV 14-APR-2021 DEFINITION Fabriciana adippe, whole genome shotgun sequencing project. ACCESSION CAJQEY000000000 VERSION CAJQEY000000000.1 DBLINK BioProject: PRJEB43991 BioSample: SAMEA7523308 KEYWORDS WGS. SOURCE Fabriciana adippe (high brown fritillary) ORGANISM Fabriciana adippe Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Argynnini; Fabriciana. REFERENCE 1 (bases 1 to 451) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Fabriciana adippe whole genome shotgun (WGS) project has the project accession CAJQEY000000000. This version of the project (01) has the accession number CAJQEY010000000, and consists of sequences CAJQEY010000001-CAJQEY010000451. The assembly ilFabAdip1.1 is based on 49x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..451 /organism="Fabriciana adippe" /mol_type="genomic DNA" /db_xref="taxon:405009" WGS CAJQEY010000001-CAJQEY010000451 // LOCUS CAJQFF010000000 568 rc DNA linear INV 14-APR-2021 DEFINITION Biston betularia, whole genome shotgun sequencing project. ACCESSION CAJQFF000000000 VERSION CAJQFF000000000.1 DBLINK BioProject: PRJEB43985 BioSample: SAMEA7520512 KEYWORDS WGS. SOURCE Biston betularia (pepper-and-salt moth) ORGANISM Biston betularia Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Biston. REFERENCE 1 (bases 1 to 568) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Biston betularia whole genome shotgun (WGS) project has the project accession CAJQFF000000000. This version of the project (01) has the accession number CAJQFF010000000, and consists of sequences CAJQFF010000001-CAJQFF010000568. The assembly ilBisBetu1.1 is based on 27x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..568 /organism="Biston betularia" /mol_type="genomic DNA" /db_xref="taxon:82595" WGS CAJQFF010000001-CAJQFF010000568 // LOCUS CAJQEV010000000 548 rc DNA linear INV 14-APR-2021 DEFINITION Plebejus argus, whole genome shotgun sequencing project. ACCESSION CAJQEV000000000 VERSION CAJQEV000000000.1 DBLINK BioProject: PRJEB44006 BioSample: SAMEA7523294 KEYWORDS WGS. SOURCE Plebejus argus ORGANISM Plebejus argus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Lycaenidae; Polyommatinae; Plebejus. REFERENCE 1 (bases 1 to 548) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Plebejus argus whole genome shotgun (WGS) project has the project accession CAJQEV000000000. This version of the project (01) has the accession number CAJQEV010000000, and consists of sequences CAJQEV010000001-CAJQEV010000548. The assembly ilPleArgu1.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..548 /organism="Plebejus argus" /mol_type="genomic DNA" /db_xref="taxon:242267" WGS CAJQEV010000001-CAJQEV010000548 // LOCUS CAJQFN010000000 234 rc DNA linear INV 14-APR-2021 DEFINITION Anthocharis cardamines, whole genome shotgun sequencing project. ACCESSION CAJQFN000000000 VERSION CAJQFN000000000.1 DBLINK BioProject: PRJEB43983 BioSample: SAMEA7523110 KEYWORDS WGS. SOURCE Anthocharis cardamines (orange tip) ORGANISM Anthocharis cardamines Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Pierinae; Anthocharis. REFERENCE 1 (bases 1 to 234) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Anthocharis cardamines whole genome shotgun (WGS) project has the project accession CAJQFN000000000. This version of the project (01) has the accession number CAJQFN010000000, and consists of sequences CAJQFN010000001-CAJQFN010000234. The assembly ilAntCard3.1 is based on 69x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..234 /organism="Anthocharis cardamines" /mol_type="genomic DNA" /db_xref="taxon:227532" WGS CAJQFN010000001-CAJQFN010000234 // LOCUS CAJQFU010000000 105 rc DNA linear INV 14-APR-2021 DEFINITION Pieris napi, whole genome shotgun sequencing project. ACCESSION CAJQFU000000000 VERSION CAJQFU000000000.1 DBLINK BioProject: PRJEB44053 BioSample: SAMEA7523287 KEYWORDS WGS. SOURCE Pieris napi ORGANISM Pieris napi Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Pierinae; Pieris. REFERENCE 1 (bases 1 to 105) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pieris napi whole genome shotgun (WGS) project has the project accession CAJQFU000000000. This version of the project (01) has the accession number CAJQFU010000000, and consists of sequences CAJQFU010000001-CAJQFU010000105. The assembly ilPieNapi1.1 is based on 60x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..105 /organism="Pieris napi" /mol_type="genomic DNA" /db_xref="taxon:78633" WGS CAJQFU010000001-CAJQFU010000105 // LOCUS CAJQFB010000000 1619 rc DNA linear INV 14-APR-2021 DEFINITION Pheosia gnoma, whole genome shotgun sequencing project. ACCESSION CAJQFB000000000 VERSION CAJQFB000000000.1 DBLINK BioProject: PRJEB44004 BioSample: SAMEA7520513 KEYWORDS WGS. SOURCE Pheosia gnoma ORGANISM Pheosia gnoma Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Notodontinae; Pheosia. REFERENCE 1 (bases 1 to 1619) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pheosia gnoma whole genome shotgun (WGS) project has the project accession CAJQFB000000000. This version of the project (01) has the accession number CAJQFB010000000, and consists of sequences CAJQFB010000001-CAJQFB010001619. The assembly ilPheGnom1.1 is based on 60x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..1619 /organism="Pheosia gnoma" /mol_type="genomic DNA" /db_xref="taxon:988018" WGS CAJQFB010000001-CAJQFB010001619 // LOCUS CAJQET010000000 507 rc DNA linear INV 14-APR-2021 DEFINITION Vespula vulgaris, whole genome shotgun sequencing project. ACCESSION CAJQET000000000 VERSION CAJQET000000000.1 DBLINK BioProject: PRJEB44007 BioSample: SAMEA7520502 KEYWORDS WGS. SOURCE Vespula vulgaris ORGANISM Vespula vulgaris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespula. REFERENCE 1 (bases 1 to 507) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespula vulgaris whole genome shotgun (WGS) project has the project accession CAJQET000000000. This version of the project (01) has the accession number CAJQET010000000, and consists of sequences CAJQET010000001-CAJQET010000507. The assembly iyVesVulg1.1 is based on 87x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..507 /organism="Vespula vulgaris" /mol_type="genomic DNA" /db_xref="taxon:7454" WGS CAJQET010000001-CAJQET010000507 // LOCUS CAJQGA010000000 331 rc DNA linear INV 14-APR-2021 DEFINITION Chrysoperla carnea, whole genome shotgun sequencing project. ACCESSION CAJQGA000000000 VERSION CAJQGA000000000.1 DBLINK BioProject: PRJEB44056 BioSample: SAMEA7520372 KEYWORDS WGS. SOURCE Chrysoperla carnea ORGANISM Chrysoperla carnea Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Neuroptera; Hemerobiiformia; Chrysopidae; Chrysopinae; Chrysoperla. REFERENCE 1 (bases 1 to 331) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Chrysoperla carnea whole genome shotgun (WGS) project has the project accession CAJQGA000000000. This version of the project (01) has the accession number CAJQGA010000000, and consists of sequences CAJQGA010000001-CAJQGA010000331. The assembly inChrCarn1.1 is based on 40x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..331 /organism="Chrysoperla carnea" /mol_type="genomic DNA" /db_xref="taxon:189513" WGS CAJQGA010000001-CAJQGA010000331 // LOCUS CAJQEZ010000000 23 rc DNA linear INV 14-APR-2021 DEFINITION Anthocharis cardamines, whole genome shotgun sequencing project. ACCESSION CAJQEZ000000000 VERSION CAJQEZ000000000.1 DBLINK BioProject: PRJEB43982 BioSample: SAMEA7523110 KEYWORDS WGS. SOURCE Anthocharis cardamines (orange tip) ORGANISM Anthocharis cardamines Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Pierinae; Anthocharis. REFERENCE 1 (bases 1 to 23) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Anthocharis cardamines whole genome shotgun (WGS) project has the project accession CAJQEZ000000000. This version of the project (01) has the accession number CAJQEZ010000000, and consists of sequences CAJQEZ010000001-CAJQEZ010000023. The assembly ilAntCard3.1 is based on 69x PacBio data, 10X Genomics Chromium data, and Qiagen Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..23 /organism="Anthocharis cardamines" /mol_type="genomic DNA" /db_xref="taxon:227532" WGS CAJQEZ010000001-CAJQEZ010000023 // LOCUS CAJQFA010000000 65 rc DNA linear INV 14-APR-2021 DEFINITION Fabriciana adippe, whole genome shotgun sequencing project. ACCESSION CAJQFA000000000 VERSION CAJQFA000000000.1 DBLINK BioProject: PRJEB43990 BioSample: SAMEA7523308 KEYWORDS WGS. SOURCE Fabriciana adippe (high brown fritillary) ORGANISM Fabriciana adippe Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Argynnini; Fabriciana. REFERENCE 1 (bases 1 to 65) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Fabriciana adippe whole genome shotgun (WGS) project has the project accession CAJQFA000000000. This version of the project (01) has the accession number CAJQFA010000000, and consists of sequences CAJQFA010000001-CAJQFA010000065. The assembly ilFabAdip1.1 is based on 49x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..65 /organism="Fabriciana adippe" /mol_type="genomic DNA" /db_xref="taxon:405009" WGS CAJQFA010000001-CAJQFA010000065 // LOCUS CADCXM020000000 58 rc DNA linear INV 14-APR-2021 DEFINITION Maniola hyperantus, whole genome shotgun sequencing project. ACCESSION CADCXM000000000 VERSION CADCXM000000000.2 DBLINK BioProject: PRJEB36756 BioSample: SAMEA994723 KEYWORDS WGS. SOURCE Maniola hyperantus (ringlet) ORGANISM Maniola hyperantus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Satyrinae; Satyrini; Maniolina; Maniola; Aphantopus. REFERENCE 1 CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (14-FEB-2020) SC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom REFERENCE 2 (bases 1 to 58) CONSRTM Wellcome Sanger Institute Data Sharing TITLE Direct Submission JOURNAL Submitted (06-APR-2021) SC, Wellcome Sanger Institute, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom COMMENT On Apr 15, 2021 this sequence version replaced CADCXM000000000.1. The Maniola hyperantus whole genome shotgun (WGS) project has the project accession CADCXM000000000. This version of the project (02) has the accession number CADCXM020000000, and consists of sequences CADCXM020000001-CADCXM020000058. The assembly iAphHyp1.2 is based on 50x PacBio data, 61x 10X Genomics Chromium data, and 81x Arima Hi-C data from a separate individual iAphHyp4 generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with purge_dups, 10X based scaffolding with scaff10x, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..58 /organism="Maniola hyperantus" /mol_type="genomic DNA" /db_xref="taxon:2795564" WGS CADCXM020000001-CADCXM020000058 // LOCUS CAJQEX010000000 15 rc DNA linear INV 14-APR-2021 DEFINITION Plebejus argus, whole genome shotgun sequencing project. ACCESSION CAJQEX000000000 VERSION CAJQEX000000000.1 DBLINK BioProject: PRJEB44005 BioSample: SAMEA7523294 KEYWORDS WGS. SOURCE Plebejus argus ORGANISM Plebejus argus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Lycaenidae; Polyommatinae; Plebejus. REFERENCE 1 (bases 1 to 15) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Plebejus argus whole genome shotgun (WGS) project has the project accession CAJQEX000000000. This version of the project (01) has the accession number CAJQEX010000000, and consists of sequences CAJQEX010000001-CAJQEX010000015. The assembly ilPleArgu1.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..15 /organism="Plebejus argus" /mol_type="genomic DNA" /db_xref="taxon:242267" WGS CAJQEX010000001-CAJQEX010000015 // LOCUS CAJQGB010000000 103 rc DNA linear INV 14-APR-2021 DEFINITION Autographa pulchrina, whole genome shotgun sequencing project. ACCESSION CAJQGB000000000 VERSION CAJQGB000000000.1 DBLINK BioProject: PRJEB44048 BioSample: SAMEA7520527 KEYWORDS WGS. SOURCE Autographa pulchrina ORGANISM Autographa pulchrina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Plusiinae; Autographa. REFERENCE 1 (bases 1 to 103) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Autographa pulchrina whole genome shotgun (WGS) project has the project accession CAJQGB000000000. This version of the project (01) has the accession number CAJQGB010000000, and consists of sequences CAJQGB010000001-CAJQGB010000103. The assembly ilAutPulc1.1 is based on 47x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..103 /organism="Autographa pulchrina" /mol_type="genomic DNA" /db_xref="taxon:987893" WGS CAJQGB010000001-CAJQGB010000103 // LOCUS CAJQFT010000000 16 rc DNA linear INV 14-APR-2021 DEFINITION Pieris napi, whole genome shotgun sequencing project. ACCESSION CAJQFT000000000 VERSION CAJQFT000000000.1 DBLINK BioProject: PRJEB44052 BioSample: SAMEA7523287 KEYWORDS WGS. SOURCE Pieris napi ORGANISM Pieris napi Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Pierinae; Pieris. REFERENCE 1 (bases 1 to 16) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pieris napi whole genome shotgun (WGS) project has the project accession CAJQFT000000000. This version of the project (01) has the accession number CAJQFT010000000, and consists of sequences CAJQFT010000001-CAJQFT010000016. The assembly ilPieNapi1.1 is based on 60x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..16 /organism="Pieris napi" /mol_type="genomic DNA" /db_xref="taxon:78633" WGS CAJQFT010000001-CAJQFT010000016 // LOCUS CAJQFG010000000 34 rc DNA linear INV 14-APR-2021 DEFINITION Glaucopsyche alexis, whole genome shotgun sequencing project. ACCESSION CAJQFG000000000 VERSION CAJQFG000000000.1 DBLINK BioProject: PRJEB43992 BioSample: SAMEA7524616 KEYWORDS WGS. SOURCE Glaucopsyche alexis (green-underside blue) ORGANISM Glaucopsyche alexis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Lycaenidae; Polyommatinae; Glaucopsyche. REFERENCE 1 (bases 1 to 34) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Glaucopsyche alexis whole genome shotgun (WGS) project has the project accession CAJQFG000000000. This version of the project (01) has the accession number CAJQFG010000000, and consists of sequences CAJQFG010000001-CAJQFG010000034. The assembly ilGlaAlex1.1 is based on 43x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..34 /organism="Glaucopsyche alexis" /mol_type="genomic DNA" /db_xref="taxon:203781" WGS CAJQFG010000001-CAJQFG010000034 // LOCUS CAJQFS010000000 2 rc DNA linear INV 14-APR-2021 DEFINITION Vespula vulgaris, whole genome shotgun sequencing project. ACCESSION CAJQFS000000000 VERSION CAJQFS000000000.1 DBLINK BioProject: PRJEB44008 BioSample: SAMEA7520502 KEYWORDS WGS. SOURCE Vespula vulgaris ORGANISM Vespula vulgaris Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Vespidae; Vespinae; Vespula. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Vespula vulgaris whole genome shotgun (WGS) project has the project accession CAJQFS000000000. This version of the project (01) has the accession number CAJQFS010000000, and consists of sequences CAJQFS010000001-CAJQFS010000002. The assembly iyVesVulg1.1 is based on 87x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Vespula vulgaris" /mol_type="genomic DNA" /db_xref="taxon:7454" WGS CAJQFS010000001-CAJQFS010000002 // LOCUS CAJQGD010000000 14 rc DNA linear INV 14-APR-2021 DEFINITION Schrankia costaestrigalis, whole genome shotgun sequencing project. ACCESSION CAJQGD000000000 VERSION CAJQGD000000000.1 DBLINK BioProject: PRJEB44055 BioSample: SAMEA7520193 KEYWORDS WGS. SOURCE Schrankia costaestrigalis (pinion-streaked snout moth) ORGANISM Schrankia costaestrigalis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Erebidae; Hypeninae; Schrankia. REFERENCE 1 (bases 1 to 14) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Schrankia costaestrigalis whole genome shotgun (WGS) project has the project accession CAJQGD000000000. This version of the project (01) has the accession number CAJQGD010000000, and consists of sequences CAJQGD010000001-CAJQGD010000014. The assembly ilSchCost1.1 is based on 38x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..14 /organism="Schrankia costaestrigalis" /mol_type="genomic DNA" /db_xref="taxon:411963" WGS CAJQGD010000001-CAJQGD010000014 // LOCUS CAJQFK010000000 8 rc DNA linear INV 14-APR-2021 DEFINITION Erannis defoliaria, whole genome shotgun sequencing project. ACCESSION CAJQFK000000000 VERSION CAJQFK000000000.1 DBLINK BioProject: PRJEB43988 BioSample: SAMEA7520367 KEYWORDS WGS. SOURCE Erannis defoliaria ORGANISM Erannis defoliaria Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Erannis. REFERENCE 1 (bases 1 to 8) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Erannis defoliaria whole genome shotgun (WGS) project has the project accession CAJQFK000000000. This version of the project (01) has the accession number CAJQFK010000000, and consists of sequences CAJQFK010000001-CAJQFK010000008. The assembly ilEraDefo1.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..8 /organism="Erannis defoliaria" /mol_type="genomic DNA" /db_xref="taxon:104474" WGS CAJQFK010000001-CAJQFK010000008 // LOCUS CAJQEW010000000 7 rc DNA linear INV 14-APR-2021 DEFINITION Pheosia gnoma, whole genome shotgun sequencing project. ACCESSION CAJQEW000000000 VERSION CAJQEW000000000.1 DBLINK BioProject: PRJEB44003 BioSample: SAMEA7520513 KEYWORDS WGS. SOURCE Pheosia gnoma ORGANISM Pheosia gnoma Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Notodontidae; Notodontinae; Pheosia. REFERENCE 1 (bases 1 to 7) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Pheosia gnoma whole genome shotgun (WGS) project has the project accession CAJQEW000000000. This version of the project (01) has the accession number CAJQEW010000000, and consists of sequences CAJQEW010000001-CAJQEW010000007. The assembly ilPheGnom1.1 is based on 60x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..7 /organism="Pheosia gnoma" /mol_type="genomic DNA" /db_xref="taxon:988018" WGS CAJQEW010000001-CAJQEW010000007 // LOCUS CAJQFZ010000000 2 rc DNA linear INV 14-APR-2021 DEFINITION Ochropleura plecta, whole genome shotgun sequencing project. ACCESSION CAJQFZ000000000 VERSION CAJQFZ000000000.1 DBLINK BioProject: PRJEB44051 BioSample: SAMEA7520524 KEYWORDS WGS. SOURCE Ochropleura plecta ORGANISM Ochropleura plecta Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Noctuinae; Noctuini; Ochropleura. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (30-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ochropleura plecta whole genome shotgun (WGS) project has the project accession CAJQFZ000000000. This version of the project (01) has the accession number CAJQFZ010000000, and consists of sequences CAJQFZ010000001-CAJQFZ010000002. The assembly ilOchPlec1.1 is based on 46x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with HiCanu, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Ochropleura plecta" /mol_type="genomic DNA" /db_xref="taxon:320037" WGS CAJQFZ010000001-CAJQFZ010000002 // LOCUS CAJQFP010000000 1 rc DNA linear INV 14-APR-2021 DEFINITION Leptidea sinapis, whole genome shotgun sequencing project. ACCESSION CAJQFP000000000 VERSION CAJQFP000000000.1 DBLINK BioProject: PRJEB43998 BioSample: SAMEA7523467 KEYWORDS WGS. SOURCE Leptidea sinapis ORGANISM Leptidea sinapis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Pieridae; Dismorphiinae; Leptidea. REFERENCE 1 (bases 1 to 1) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Leptidea sinapis whole genome shotgun (WGS) project has the project accession CAJQFP000000000. This version of the project (01) has the accession number CAJQFP010000000, and consists of sequence CAJQFP010000001. The assembly ilLepSina1.1 is based on 36x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1 /organism="Leptidea sinapis" /mol_type="genomic DNA" /db_xref="taxon:189913" /note="contig: scaffold_59_ctg1" WGS CAJQFP010000001 // LOCUS CAJQEU010000000 1 rc DNA linear INV 14-APR-2021 DEFINITION Biston betularia, whole genome shotgun sequencing project. ACCESSION CAJQEU000000000 VERSION CAJQEU000000000.1 DBLINK BioProject: PRJEB43984 BioSample: SAMEA7520512 KEYWORDS WGS. SOURCE Biston betularia (pepper-and-salt moth) ORGANISM Biston betularia Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Biston. REFERENCE 1 (bases 1 to 1) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Biston betularia whole genome shotgun (WGS) project has the project accession CAJQEU000000000. This version of the project (01) has the accession number CAJQEU010000000, and consists of sequence CAJQEU010000001. The assembly ilBisBetu1.1 is based on 27x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1 /organism="Biston betularia" /mol_type="genomic DNA" /db_xref="taxon:82595" /note="contig: scaffold_39_ctg1" WGS CAJQEU010000001 // LOCUS CAJQFC010000000 938 rc DNA linear INV 14-APR-2021 DEFINITION Ochlodes sylvanus, whole genome shotgun sequencing project. ACCESSION CAJQFC000000000 VERSION CAJQFC000000000.1 DBLINK BioProject: PRJEB44001 BioSample: SAMEA7523138 KEYWORDS WGS. SOURCE Ochlodes sylvanus ORGANISM Ochlodes sylvanus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Ochlodes. REFERENCE 1 (bases 1 to 938) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ochlodes sylvanus whole genome shotgun (WGS) project has the project accession CAJQFC000000000. This version of the project (01) has the accession number CAJQFC010000000, and consists of sequences CAJQFC010000001-CAJQFC010000938. The assembly ilOchSylv3.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..938 /organism="Ochlodes sylvanus" /mol_type="genomic DNA" /db_xref="taxon:876063" WGS CAJQFC010000001-CAJQFC010000938 // LOCUS CAJQFI010000000 195 rc DNA linear INV 14-APR-2021 DEFINITION Hesperia comma, whole genome shotgun sequencing project. ACCESSION CAJQFI000000000 VERSION CAJQFI000000000.1 DBLINK BioProject: PRJEB43997 BioSample: SAMEA7523119 KEYWORDS WGS. SOURCE Hesperia comma (common branded skipper) ORGANISM Hesperia comma Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Hesperia. REFERENCE 1 (bases 1 to 195) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hesperia comma whole genome shotgun (WGS) project has the project accession CAJQFI000000000. This version of the project (01) has the accession number CAJQFI010000000, and consists of sequences CAJQFI010000001-CAJQFI010000195. The assembly ilHesComm1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..195 /organism="Hesperia comma" /mol_type="genomic DNA" /db_xref="taxon:291688" WGS CAJQFI010000001-CAJQFI010000195 // LOCUS CAJQFD010000000 10 rc DNA linear INV 14-APR-2021 DEFINITION Hesperia comma, whole genome shotgun sequencing project. ACCESSION CAJQFD000000000 VERSION CAJQFD000000000.1 DBLINK BioProject: PRJEB43996 BioSample: SAMEA7523119 KEYWORDS WGS. SOURCE Hesperia comma (common branded skipper) ORGANISM Hesperia comma Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Hesperia. REFERENCE 1 (bases 1 to 10) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Hesperia comma whole genome shotgun (WGS) project has the project accession CAJQFD000000000. This version of the project (01) has the accession number CAJQFD010000000, and consists of sequences CAJQFD010000001-CAJQFD010000010. The assembly ilHesComm1.1 is based on 28x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..10 /organism="Hesperia comma" /mol_type="genomic DNA" /db_xref="taxon:291688" WGS CAJQFD010000001-CAJQFD010000010 // LOCUS CAJQFO010000000 2 rc DNA linear INV 14-APR-2021 DEFINITION Ochlodes sylvanus, whole genome shotgun sequencing project. ACCESSION CAJQFO000000000 VERSION CAJQFO000000000.1 DBLINK BioProject: PRJEB44002 BioSample: SAMEA7523138 KEYWORDS WGS. SOURCE Ochlodes sylvanus ORGANISM Ochlodes sylvanus Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Hesperioidea; Hesperiidae; Hesperiinae; Hesperiini; Ochlodes. REFERENCE 1 (bases 1 to 2) CONSRTM Wellcome Sanger Tree of Life Programme TITLE Direct Submission JOURNAL Submitted (29-MAR-2021) WELLCOME SANGER INSTITUTE, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom COMMENT The Ochlodes sylvanus whole genome shotgun (WGS) project has the project accession CAJQFO000000000. This version of the project (01) has the accession number CAJQFO010000000, and consists of sequences CAJQFO010000001-CAJQFO010000002. The assembly ilOchSylv3.1 is based on 23x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. FEATURES Location/Qualifiers source 1..2 /organism="Ochlodes sylvanus" /mol_type="genomic DNA" /db_xref="taxon:876063" WGS CAJQFO010000001-CAJQFO010000002 // LOCUS AZAI02000000 14526 rc DNA linear INV 13-APR-2021 DEFINITION Eurytemora affinis strain Atlantic clade, whole genome shotgun sequencing project. ACCESSION AZAI00000000 VERSION AZAI00000000.2 DBLINK BioProject: PRJNA203087 BioSample: SAMN02302763 KEYWORDS WGS. SOURCE Eurytemora affinis ORGANISM Eurytemora affinis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Multicrustacea; Hexanauplia; Copepoda; Calanoida; Temoridae; Eurytemora. REFERENCE 1 (bases 1 to 14526) AUTHORS Eyun,S.I., Soh,H.Y., Posavi,M., Munro,J.B., Hughes,D.S.T., Murali,S.C., Qu,J., Dugan,S., Lee,S.L., Chao,H., Dinh,H., Han,Y., Doddapaneni,H., Worley,K.C., Muzny,D.M., Park,E.O., Silva,J.C., Gibbs,R.A., Richards,S. and Lee,C.E. TITLE Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda JOURNAL Mol Biol Evol 34 (8), 1838-1862 (2017) PUBMED 28460028 REFERENCE 2 (bases 1 to 14526) AUTHORS Murali,S.C., Bandaranaike,D., Bellair,M., Blankenburg,K., Chao,H., Dinh,H., Doddapaneni,H., Dugan-Rocha,S., Elkadiri,S., Gnanaolivu,R.D., Hernandez,B., Javaid,M., Jayaseelan,J.C., Lee,S., Li,M., Ming,W., Munidasa,M., Muniz,J., Nguyen,L., Ongeri,F., Osuji,N., Pu,L.-L., Puazo,M., Qu,C., Quiroz,J., Raj,R., Weissenberger,G., Xin,Y., Zou,X., Han,Y., Richards,S., Worley,K., Muzny,D. and Gibbs,R. TITLE Direct Submission JOURNAL Submitted (19-NOV-2013) Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA REFERENCE 3 (bases 1 to 14526) AUTHORS Murali,S., Richards,S., Bandaranaike,D., Bellair,M., Blankenburg,K., Chao,H., Dinh,H., Doddapaneni,H., Dugan-Rocha,S., Elkadiri,S., Gnanaolivu,R., Hughes,D., Lee,S., Li,M., Ming,W., Munidasa,M., Muniz,J., Nguyen,L., Osuji,N., Pu,L.-L., Puazo,M., Skinner,E., Qu,C., Quiroz,J., Raj,R., Weissenberger,G., Xin,Y., Zou,X., Han,Y., Worley,K., Muzny,D. and Gibbs,R. TITLE Direct Submission JOURNAL Submitted (09-OCT-2017) Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA COMMENT On Dec 12, 2017 this sequence version replaced AZAI00000000.1. The Eurytemora affinis whole genome shotgun (WGS) project has the project accession AZAI00000000. This version of the project (02) has the accession number AZAI02000000, and consists of sequences AZAI02000001-AZAI02014526. ##Genome-Assembly-Data-START## Assembly Date :: APR-2016 Assembly Method :: AllPaths LG v. 44620; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2; redundans v. 0.12c Assembly Name :: Eaff_2.0 Expected Final Version :: no Genome Coverage :: 75.0x Sequencing Technology :: Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..14526 /organism="Eurytemora affinis" /mol_type="genomic DNA" /strain="Atlantic clade" /isolation_source="salt marsh" /db_xref="taxon:88015" /dev_stage="egg" /country="Canada: Baie de L'Isle Verte, St. Lawrence estuary (salt marsh), Quebec" /collection_date="2006/2007" WGS AZAI02000001-AZAI02014526 WGS_SCAFLD KZ484133-KZ486246 // LOCUS JAEANM010000000 297074 rc DNA linear VRT 01-APR-2021 DEFINITION Myanophis thanlyinensis isolate TSch-2020a, whole genome shotgun sequencing project. ACCESSION JAEANM000000000 VERSION JAEANM000000000.1 DBLINK BioProject: PRJNA667001 BioSample: SAMN16348494 KEYWORDS WGS. SOURCE Myanophis thanlyinensis ORGANISM Myanophis thanlyinensis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Serpentes; Colubroidea; Homalopsidae; Myanophis. REFERENCE 1 (bases 1 to 297074) AUTHORS Kohler,G., Khaing,K.P.P., Than,N.L., Baranski,D., Schell,T., Greve,C., Janke,A. and Pauls,S.U. TITLE A new genus and species of mud snake from Myanmar (Reptilia, Squamata, Homalopsidae) JOURNAL Zootaxa 4915 (3), zootaxa.4915.3.1 (2021) PUBMED 33756559 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 297074) AUTHORS Schell,T. TITLE Direct Submission JOURNAL Submitted (26-NOV-2020) Senckenberg Biodiversity Genome Collection, LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, Frankfurt am Main 60325, Germany COMMENT The Myanophis thanlyinensis whole genome shotgun (WGS) project has the project accession JAEANM000000000. This version of the project (01) has the accession number JAEANM010000000, and consists of sequences JAEANM010000001-JAEANM010297074. ##Genome-Assembly-Data-START## Assembly Date :: 03-NOV-2020 Assembly Method :: SPAdes v. 3.14.1 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 81.0x Sequencing Technology :: Illumina NovaSeq ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..297074 /organism="Myanophis thanlyinensis" /mol_type="genomic DNA" /isolate="TSch-2020a" /db_xref="taxon:2777982" /sex="male" /tissue_type="tongue" /dev_stage="adult" /country="Myanmar: Yangon, Thanlyin, near East Yangon University" /lat_lon="16.74255 N 96.28307 E" /collection_date="2019-11-05" /collected_by="Ni Lar Than & Gunther Khler" WGS JAEANM010000001-JAEANM010297074 // LOCUS WNMJ02000000 5626 rc DNA linear VRT 30-MAR-2021 DEFINITION Cygnus olor isolate bCygOlo1, whole genome shotgun sequencing project. ACCESSION WNMJ00000000 VERSION WNMJ00000000.2 DBLINK BioProject: PRJNA561961 BioSample: SAMN12621369 KEYWORDS WGS. SOURCE Cygnus olor (mute swan) ORGANISM Cygnus olor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Anseriformes; Anatidae; Anserinae; Cygnus. REFERENCE 1 (bases 1 to 5626) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Cygnus olor (Mute swan) genome, bCygOlo1, alternate haplotype, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 5626) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (14-NOV-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 5626) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (13-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Mar 30, 2021 this sequence version replaced WNMJ00000000.1. The Cygnus olor whole genome shotgun (WGS) project has the project accession WNMJ00000000. This version of the project (02) has the accession number WNMJ02000000, and consists of sequences WNMJ02000001-WNMJ02005626. ##Genome-Assembly-Data-START## Assembly Date :: 30-NOV-2020 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 6.0.0.47841; purge_haplotigs v. 1.0.3+ 1.Nov.2018; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2020-11-30; VGP assembly pipeline individual v. 1.5 Assembly Name :: bCygOlo1.alt.v2 Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.23x Sequencing Technology :: PacBio Sequel; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..5626 /organism="Cygnus olor" /mol_type="genomic DNA" /isolate="bCygOlo1" /db_xref="taxon:8869" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="Germany: Mainau" /lat_lon="50.149850 N 11.063270 E" /collection_date="2015-07-01" /collected_by="Robert Kraus" WGS WNMJ02000001-WNMJ02005626 // LOCUS WNMI02000000 171 rc DNA linear VRT 31-MAR-2021 DEFINITION Cygnus olor isolate bCygOlo1, whole genome shotgun sequencing project. ACCESSION WNMI00000000 VERSION WNMI00000000.2 DBLINK BioProject: PRJNA561960 BioSample: SAMN12621369 KEYWORDS WGS. SOURCE Cygnus olor (mute swan) ORGANISM Cygnus olor Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Anseriformes; Anatidae; Anserinae; Cygnus. REFERENCE 1 (bases 1 to 171) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Cygnus olor (Mute swan) genome, bCygOlo1, primary haplotype, v2 JOURNAL Unpublished REFERENCE 2 (bases 1 to 171) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (14-NOV-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA REFERENCE 3 (bases 1 to 171) AUTHORS Kraus,R., Fedrigo,O., Formenti,G., Mountcastle,J., Chow,W., Collins,J., Howe,K., Rhie,A., Karawita,A., Short,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (13-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT On Mar 30, 2021 this sequence version replaced WNMI00000000.1. The Cygnus olor whole genome shotgun (WGS) project has the project accession WNMI00000000. This version of the project (02) has the accession number WNMI02000000, and consists of sequences WNMI02000001-WNMI02000171. ##Genome-Assembly-Data-START## Assembly Date :: 30-NOV-2020 Assembly Method :: FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 6.0.0.47841; purge_haplotigs v. 1.0.3+ 1.Nov.2018; scaff10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 6.0.0.47841; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2020-11-30; VGP assembly pipeline individual v. 1.5 Assembly Name :: bCygOlo1.pri.v2 Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.23x Sequencing Technology :: PacBio Sequel 1 CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..171 /organism="Cygnus olor" /mol_type="genomic DNA" /isolate="bCygOlo1" /db_xref="taxon:8869" /sex="male" /tissue_type="muscle" /dev_stage="adult" /country="Germany: Mainau" /lat_lon="50.149850 N 11.063270 E" /collection_date="2015-07-01" /collected_by="Robert Kraus" WGS WNMI02000001-WNMI02000171 WGS_SCAFLD CM020065-CM020095 WGS_SCAFLD CM020139 WGS_SCAFLD CM030310-CM030314 // LOCUS JAGFOW010000000 5690 rc DNA linear VRT 30-MAR-2021 DEFINITION Aplochiton taeniatus isolate fAplTae1, whole genome shotgun sequencing project. ACCESSION JAGFOW000000000 VERSION JAGFOW000000000.1 DBLINK BioProject: PRJNA561972 BioSample: SAMN12623621 KEYWORDS WGS. SOURCE Aplochiton taeniatus ORGANISM Aplochiton taeniatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Galaxiidae; Aplochiton. REFERENCE 1 (bases 1 to 5690) AUTHORS Myers,G., Pippel,M., Formenti,G., Montero,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Guzman,C.C., Meyer,A., Durbin,R., Venkatesh,B. and Jarvis,E.D. TITLE Aplochiton taeniatus (Peladilla) genome, fAplTae1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 5690) AUTHORS Myers,G., Pippel,M., Formenti,G., Montero,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Guzman,C.C., Meyer,A., Durbin,R., Venkatesh,B. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Aplochiton taeniatus whole genome shotgun (WGS) project has the project accession JAGFOW000000000. This version of the project (01) has the accession number JAGFOW010000000, and consists of sequences JAGFOW010000001-JAGFOW010005690. ##Genome-Assembly-Data-START## Assembly Date :: 04-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; Assembly Polish v. SMRTLink7.0.1; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-04; VGP assembly pipeline v. 1.6 Assembly Name :: fAplTae1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..5690 /organism="Aplochiton taeniatus" /mol_type="genomic DNA" /isolate="fAplTae1" /specimen_voucher="6995" /db_xref="taxon:946358" /tissue_type="liver" /dev_stage="subadult" /country="Chile: Santo Domingo River, Valdivia, Los Rios district" /lat_lon="39.917592 S 73.107197 W" /collection_date="2018-09-11" /collected_by="Cristian Correa Guzman" WGS JAGFOW010000001-JAGFOW010005690 // LOCUS JAGFVO010000000 4278 rc DNA linear VRT 30-MAR-2021 DEFINITION Ciconia maguari isolate bCicMag1, whole genome shotgun sequencing project. ACCESSION JAGFVO000000000 VERSION JAGFVO000000000.1 DBLINK BioProject: PRJNA715732 BioSample: SAMN18353822 KEYWORDS WGS. SOURCE Ciconia maguari ORGANISM Ciconia maguari Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Ciconiiformes; Ciconiidae; Ciconia. REFERENCE 1 (bases 1 to 4278) AUTHORS Gilbert,M.T.P., De Panis,D., Formenti,G., Pelan,S., Sims,Y., Angie,J., Chiappe,L., Olson,S., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Ciconia maguari (Maguari stork) genome, bCicMag1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 4278) AUTHORS Gilbert,M.T.P., De Panis,D., Formenti,G., Pelan,S., Sims,Y., Angie,J., Chiappe,L., Olson,S., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Ciconia maguari whole genome shotgun (WGS) project has the project accession JAGFVO000000000. This version of the project (01) has the accession number JAGFVO010000000, and consists of sequences JAGFVO010000001-JAGFVO010004278. ##Genome-Assembly-Data-START## Assembly Date :: 15-JUL-2020 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2020-07-15; VGP assembly pipeline v. 1.6 Assembly Name :: bCicMag1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 88.32x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..4278 /organism="Ciconia maguari" /mol_type="genomic DNA" /isolate="bCicMag1" /specimen_voucher="USNM:614528" /db_xref="taxon:52777" /sex="female" /dev_stage="adult" /country="Argentina: Estancia El Tala, near Puerto Constanza" /lat_lon="33.2599 S 64.8519 W" /collection_date="1992-02-18" /collected_by="J.P. Angie, Luis Chiappe, Storrs L. Olsonn" WGS JAGFVO010000001-JAGFVO010004278 // LOCUS JAGFVJ010000000 3194 rc DNA linear VRT 30-MAR-2021 DEFINITION Melanotaenia boesemani isolate fMelBoe1, whole genome shotgun sequencing project. ACCESSION JAGFVJ000000000 VERSION JAGFVJ000000000.1 DBLINK BioProject: PRJNA561966 BioSample: SAMN12623618 KEYWORDS WGS. SOURCE Melanotaenia boesemani (Boeseman's rainbowfish) ORGANISM Melanotaenia boesemani Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Atherinomorphae; Atheriniformes; Melanotaeniidae; Melanotaenia. REFERENCE 1 (bases 1 to 3194) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Melanotaenia boesemani (Boeseman's rainbowfish) genome, fMelBoe1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 3194) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (20-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Melanotaenia boesemani whole genome shotgun (WGS) project has the project accession JAGFVJ000000000. This version of the project (01) has the accession number JAGFVJ010000000, and consists of sequences JAGFVJ010000001-JAGFVJ010003194. ##Genome-Assembly-Data-START## Assembly Date :: 12-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-12; VGP assembly pipeline v. 1.6 Assembly Name :: fMelBoe1.alt Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..3194 /organism="Melanotaenia boesemani" /mol_type="genomic DNA" /isolate="fMelBoe1" /db_xref="taxon:1250792" /tissue_type="muscle" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-08" /collected_by="Byrappa Venkatesh" WGS JAGFVJ010000001-JAGFVJ010003194 // LOCUS JAGFVI010000000 93 rc DNA linear VRT 30-MAR-2021 DEFINITION Melanotaenia boesemani isolate fMelBoe1, whole genome shotgun sequencing project. ACCESSION JAGFVI000000000 VERSION JAGFVI000000000.1 DBLINK BioProject: PRJNA561965 BioSample: SAMN12623618 KEYWORDS WGS. SOURCE Melanotaenia boesemani (Boeseman's rainbowfish) ORGANISM Melanotaenia boesemani Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Atherinomorphae; Atheriniformes; Melanotaeniidae; Melanotaenia. REFERENCE 1 (bases 1 to 93) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Melanotaenia boesemani (Boeseman's rainbowfish) genome, fMelBoe1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 93) AUTHORS Myers,G., Brown,T., Pippel,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Venkatesh,B., Durbin,R. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (20-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Melanotaenia boesemani whole genome shotgun (WGS) project has the project accession JAGFVI000000000. This version of the project (01) has the accession number JAGFVI010000000, and consists of sequences JAGFVI010000001-JAGFVI010000093. ##Genome-Assembly-Data-START## Assembly Date :: 12-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-12; VGP assembly pipeline v. 1.6 Assembly Name :: fMelBoe1.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..93 /organism="Melanotaenia boesemani" /mol_type="genomic DNA" /isolate="fMelBoe1" /db_xref="taxon:1250792" /tissue_type="muscle" /country="Singapore" /lat_lon="1.3521 N 103.8198 E" /collection_date="2018-08-08" /collected_by="Byrappa Venkatesh" WGS JAGFVI010000001-JAGFVI010000093 WGS_SCAFLD CM030225-CM030249 // LOCUS JAGFOV010000000 41 rc DNA linear VRT 30-MAR-2021 DEFINITION Aplochiton taeniatus isolate fAplTae1, whole genome shotgun sequencing project. ACCESSION JAGFOV000000000 VERSION JAGFOV000000000.1 DBLINK BioProject: PRJNA561971 BioSample: SAMN12623621 KEYWORDS WGS. SOURCE Aplochiton taeniatus ORGANISM Aplochiton taeniatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Galaxiidae; Aplochiton. REFERENCE 1 (bases 1 to 41) AUTHORS Myers,G., Pippel,M., Formenti,G., Montero,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Guzman,C.C., Meyer,A., Durbin,R., Venkatesh,B. and Jarvis,E.D. TITLE Aplochiton taeniatus (Peladilla) genome, fAplTae1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 41) AUTHORS Myers,G., Pippel,M., Formenti,G., Montero,M., Winkler,S., Tracey,A., Pointon,D.-L., Howe,K., Guzman,C.C., Meyer,A., Durbin,R., Venkatesh,B. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (19-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Aplochiton taeniatus whole genome shotgun (WGS) project has the project accession JAGFOV000000000. This version of the project (01) has the accession number JAGFOV010000000, and consists of sequences JAGFOV010000001-JAGFOV010000041. ##Genome-Assembly-Data-START## Assembly Date :: 04-MAR-2021 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; Assembly Polish v. SMRTLink7.0.1; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-04; VGP assembly pipeline v. 1.6 Assembly Name :: fAplTae1.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..41 /organism="Aplochiton taeniatus" /mol_type="genomic DNA" /isolate="fAplTae1" /specimen_voucher="6995" /db_xref="taxon:946358" /tissue_type="liver" /dev_stage="subadult" /country="Chile: Santo Domingo River, Valdivia, Los Rios district" /lat_lon="39.917592 S 73.107197 W" /collection_date="2018-09-11" /collected_by="Cristian Correa Guzman" WGS JAGFOV010000001-JAGFOV010000041 WGS_SCAFLD CM030172-CM030191 // LOCUS JAGFVT010000000 551 rc DNA linear VRT 30-MAR-2021 DEFINITION Falco naumanni isolate bFalNau1, whole genome shotgun sequencing project. ACCESSION JAGFVT000000000 VERSION JAGFVT000000000.1 DBLINK BioProject: PRJNA702665 BioSample: SAMN16870685 KEYWORDS WGS. SOURCE Falco naumanni (lesser kestrel) ORGANISM Falco naumanni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Falconiformes; Falconidae; Falco. REFERENCE 1 (bases 1 to 551) AUTHORS Rubolini,D., Formenti,G., Secomandi,S., Maloney,B., Bounas,T., Mountcastle,J., Haase,B., Bonisoli-Alquati,A., Galimberti,A., Ficetola,G.F., Tracey,A., Sims,Y., Howe,K., Rhie,A., Fedrigo,O. and Jarvis,E.D. TITLE Falco naumanni (Lesser kestrel) genome, bFalNau1, maternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 551) AUTHORS Rubolini,D., Formenti,G., Secomandi,S., Maloney,B., Bounas,T., Mountcastle,J., Haase,B., Bonisoli-Alquati,A., Galimberti,A., Ficetola,G.F., Tracey,A., Sims,Y., Howe,K., Rhie,A., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (18-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Falco naumanni whole genome shotgun (WGS) project has the project accession JAGFVT000000000. This version of the project (01) has the accession number JAGFVT010000000, and consists of sequences JAGFVT010000001-JAGFVT010000551. ##Genome-Assembly-Data-START## Assembly Date :: 14-JUL-2020 Assembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; pbgcpp v. 1.9.0; Freebayes v. 1.3.1; gEVAL manual curation v. 2020-07-14; VGP trio assembly pipeline v. 1.6 Assembly Name :: bFalNau1.mat Diploid :: Alternate pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 104.34x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..551 /organism="Falco naumanni" /mol_type="genomic DNA" /isolate="bFalNau1" /specimen_voucher="P51P2 - H187058 (nest 2016-P51)" /db_xref="taxon:148594" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="Italy: Matera" /lat_lon="40.67 N 16.60 E" /collection_date="2016-06-25" /collected_by="Diego Rubolini" WGS JAGFVT010000001-JAGFVT010000551 // LOCUS JAGFVN010000000 153 rc DNA linear VRT 30-MAR-2021 DEFINITION Ciconia maguari isolate bCicMag1, whole genome shotgun sequencing project. ACCESSION JAGFVN000000000 VERSION JAGFVN000000000.1 DBLINK BioProject: PRJNA715733 BioSample: SAMN18353822 KEYWORDS WGS. SOURCE Ciconia maguari ORGANISM Ciconia maguari Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Ciconiiformes; Ciconiidae; Ciconia. REFERENCE 1 (bases 1 to 153) AUTHORS Gilbert,M.T.P., De Panis,D., Formenti,G., Pelan,S., Sims,Y., Angie,J., Chiappe,L., Olson,S., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Ciconia maguari (Maguari stork) genome, bCicMag1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 153) AUTHORS Gilbert,M.T.P., De Panis,D., Formenti,G., Pelan,S., Sims,Y., Angie,J., Chiappe,L., Olson,S., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (23-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Ciconia maguari whole genome shotgun (WGS) project has the project accession JAGFVN000000000. This version of the project (01) has the accession number JAGFVN010000000, and consists of sequences JAGFVN010000001-JAGFVN010000153. ##Genome-Assembly-Data-START## Assembly Date :: 15-JUL-2020 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2020-07-15; VGP assembly pipeline v. 1.6 Assembly Name :: bCicMag1.pri Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 88.32x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..153 /organism="Ciconia maguari" /mol_type="genomic DNA" /isolate="bCicMag1" /specimen_voucher="USNM:614528" /db_xref="taxon:52777" /sex="female" /dev_stage="adult" /country="Argentina: Estancia El Tala, near Puerto Constanza" /lat_lon="33.2599 S 64.8519 W" /collection_date="1992-02-18" /collected_by="J.P. Angie, Luis Chiappe, Storrs L. Olsonn" WGS JAGFVN010000001-JAGFVN010000153 WGS_SCAFLD CM030193-CM030224 // LOCUS JAGFVS010000000 291 rc DNA linear VRT 30-MAR-2021 DEFINITION Falco naumanni isolate bFalNau1, whole genome shotgun sequencing project. ACCESSION JAGFVS000000000 VERSION JAGFVS000000000.1 DBLINK BioProject: PRJNA702666 BioSample: SAMN16870685 KEYWORDS WGS. SOURCE Falco naumanni (lesser kestrel) ORGANISM Falco naumanni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Falconiformes; Falconidae; Falco. REFERENCE 1 (bases 1 to 291) AUTHORS Rubolini,D., Formenti,G., Secomandi,S., Maloney,B., Bounas,T., Mountcastle,J., Haase,B., Bonisoli-Alquati,A., Galimberti,A., Ficetola,G.F., Tracey,A., Sims,Y., Howe,K., Rhie,A., Fedrigo,O. and Jarvis,E.D. TITLE Falco naumanni (Lesser kestrel) genome, bFalNau1, paternal haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 291) AUTHORS Rubolini,D., Formenti,G., Secomandi,S., Maloney,B., Bounas,T., Mountcastle,J., Haase,B., Bonisoli-Alquati,A., Galimberti,A., Ficetola,G.F., Tracey,A., Sims,Y., Howe,K., Rhie,A., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (18-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Falco naumanni whole genome shotgun (WGS) project has the project accession JAGFVS000000000. This version of the project (01) has the accession number JAGFVS010000000, and consists of sequences JAGFVS010000001-JAGFVS010000291. ##Genome-Assembly-Data-START## Assembly Date :: 14-JUL-2020 Assembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; pbgcpp v. 1.9.0; Freebayes v. 1.3.1; gEVAL manual curation v. 2020-07-14; VGP trio assembly pipeline v. 1.6 Assembly Name :: bFalNau1.pat Diploid :: Principal pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 104.34x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..291 /organism="Falco naumanni" /mol_type="genomic DNA" /isolate="bFalNau1" /specimen_voucher="P51P2 - H187058 (nest 2016-P51)" /db_xref="taxon:148594" /sex="female" /tissue_type="blood" /dev_stage="juvenile" /country="Italy: Matera" /lat_lon="40.67 N 16.60 E" /collection_date="2016-06-25" /collected_by="Diego Rubolini" WGS JAGFVS010000001-JAGFVS010000291 WGS_SCAFLD CM030145-CM030171 WGS_SCAFLD CM030192 // LOCUS JAGDEE010000000 719 rc DNA linear VRT 30-MAR-2021 DEFINITION Carcharodon carcharias isolate sCarCar2, whole genome shotgun sequencing project. ACCESSION JAGDEE000000000 VERSION JAGDEE000000000.1 DBLINK BioProject: PRJNA562007 BioSample: SAMN12629504 KEYWORDS WGS. SOURCE Carcharodon carcharias (great white shark) ORGANISM Carcharodon carcharias Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Lamniformes; Alopiidae; Carcharodon. REFERENCE 1 (bases 1 to 719) AUTHORS Naylor,G., Fedrigo,O., Lowe,C., Lyons,K., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K. and Jarvis,E.D. TITLE Carcharodon carcharias (Great white shark) genome, sCarCar2, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 719) AUTHORS Naylor,G., Fedrigo,O., Lowe,C., Lyons,K., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (10-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Carcharodon carcharias whole genome shotgun (WGS) project has the project accession JAGDEE000000000. This version of the project (01) has the accession number JAGDEE010000000, and consists of sequences JAGDEE010000001-JAGDEE010000719. ##Genome-Assembly-Data-START## Assembly Date :: 05-FEB-2021 Assembly Method :: FALCON v. DX 2.0.1; FALCON-Unzip v. DX 1.2.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; Arrow polishing and gap filling v. DX 7.0.1.1; Longranger Align DX v. 2.2.2.1; freebayes DX v. 19-07-11; gEVAL manual curation v. 2021-02-05; VGP assembly pipeline v. 1.6 Assembly Name :: sCarCar2.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 66.84x Sequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..719 /organism="Carcharodon carcharias" /mol_type="genomic DNA" /isolate="sCarCar2" /db_xref="taxon:13397" /sex="male" /tissue_type="blood" /dev_stage="juvenile" /country="USA" /lat_lon="33.782158 N 118.12249 W" /collection_date="2019-01-30" /collected_by="Chris Lowe, Kady Lyons" WGS JAGDEE010000001-JAGDEE010000719 WGS_SCAFLD CM029965-CM030006 WGS_SCAFLD CM030070 // LOCUS JAGGDW010000000 1147 rc DNA linear VRT 30-MAR-2021 DEFINITION Pluvialis apricaria isolate bPluApr1, whole genome shotgun sequencing project. ACCESSION JAGGDW000000000 VERSION JAGGDW000000000.1 DBLINK BioProject: PRJNA715923 BioSample: SAMN18353970 KEYWORDS WGS. SOURCE Pluvialis apricaria ORGANISM Pluvialis apricaria Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Charadriiformes; Charadriidae; Pluvialis. REFERENCE 1 (bases 1 to 1147) AUTHORS Gilbert,M.T.P., Fungtammasan,A., Secomandi,S., Formenti,G., Collins,J., Wood,J., Dove,C.J., Graves,G., Durbin,R., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Pluvialis apricaria (European golden plover) genome, bPluApr1, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 1147) AUTHORS Gilbert,M.T.P., Fungtammasan,A., Secomandi,S., Formenti,G., Collins,J., Wood,J., Dove,C.J., Graves,G., Durbin,R., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (23-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Pluvialis apricaria whole genome shotgun (WGS) project has the project accession JAGGDW000000000. This version of the project (01) has the accession number JAGGDW010000000, and consists of sequences JAGGDW010000001-JAGGDW010001147. ##Genome-Assembly-Data-START## Assembly Date :: 28-JUL-2020 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2020-07-28; VGP assembly pipeline v. 1.6 Assembly Name :: bPluApr1.alt Diploid :: Alternate Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..1147 /organism="Pluvialis apricaria" /mol_type="genomic DNA" /isolate="bPluApr1" /specimen_voucher="USNM:614528" /db_xref="taxon:670352" /sex="female" /dev_stage="adult" /country="Iceland: Keflavik Naval Air Station" /lat_lon="63.971667 N 22.601111 W" /collection_date="2001-08-07" /collected_by="Carla J. Dove" WGS JAGGDW010000001-JAGGDW010001147 // LOCUS JAGGDV010000000 107 rc DNA linear VRT 30-MAR-2021 DEFINITION Pluvialis apricaria isolate bPluApr1, whole genome shotgun sequencing project. ACCESSION JAGGDV000000000 VERSION JAGGDV000000000.1 DBLINK BioProject: PRJNA715924 BioSample: SAMN18353970 KEYWORDS WGS. SOURCE Pluvialis apricaria ORGANISM Pluvialis apricaria Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Charadriiformes; Charadriidae; Pluvialis. REFERENCE 1 (bases 1 to 107) AUTHORS Gilbert,M.T.P., Fungtammasan,A., Secomandi,S., Formenti,G., Collins,J., Wood,J., Dove,C.J., Graves,G., Durbin,R., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Pluvialis apricaria (European golden plover) genome, bPluApr1, primary haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 107) AUTHORS Gilbert,M.T.P., Fungtammasan,A., Secomandi,S., Formenti,G., Collins,J., Wood,J., Dove,C.J., Graves,G., Durbin,R., Howe,K., Fedrigo,O. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (23-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Pluvialis apricaria whole genome shotgun (WGS) project has the project accession JAGGDV000000000. This version of the project (01) has the accession number JAGGDV010000000, and consists of sequences JAGGDV010000001-JAGGDV010000107. ##Genome-Assembly-Data-START## Assembly Date :: 28-JUL-2020 Assembly Method :: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2020-07-15; VGP assembly pipeline v. 1.6 Assembly Name :: bPluApr1.pri Diploid :: Principal Pseudohaplotype Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 60.0x Sequencing Technology :: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..107 /organism="Pluvialis apricaria" /mol_type="genomic DNA" /isolate="bPluApr1" /specimen_voucher="USNM:614528" /db_xref="taxon:670352" /sex="female" /dev_stage="adult" /country="Iceland: Keflavik Naval Air Station" /lat_lon="63.971667 N 22.601111 W" /collection_date="2001-08-07" /collected_by="Carla J. Dove" WGS JAGGDV010000001-JAGGDV010000107 WGS_SCAFLD CM030007-CM030045 // LOCUS JAGDEF010000000 39 rc DNA linear VRT 30-MAR-2021 DEFINITION Carcharodon carcharias isolate sCarCar2, whole genome shotgun sequencing project. ACCESSION JAGDEF000000000 VERSION JAGDEF000000000.1 DBLINK BioProject: PRJNA562008 BioSample: SAMN12629504 KEYWORDS WGS. SOURCE Carcharodon carcharias (great white shark) ORGANISM Carcharodon carcharias Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Lamniformes; Alopiidae; Carcharodon. REFERENCE 1 (bases 1 to 39) AUTHORS Naylor,G., Fedrigo,O., Lowe,C., Lyons,K., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K. and Jarvis,E.D. TITLE Carcharodon carcharias (Great white shark) genome, sCarCar2, alternate haplotype JOURNAL Unpublished REFERENCE 2 (bases 1 to 39) AUTHORS Naylor,G., Fedrigo,O., Lowe,C., Lyons,K., Formenti,G., Tracey,A., Pointon,D.-L., Howe,K. and Jarvis,E.D. TITLE Direct Submission JOURNAL Submitted (10-MAR-2021) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA COMMENT The Carcharodon carcharias whole genome shotgun (WGS) project has the project accession JAGDEF000000000. This version of the project (01) has the accession number JAGDEF010000000, and consists of sequences JAGDEF010000001-JAGDEF010000039. ##Genome-Assembly-Data-START## Assembly Date :: 05-FEB-2021 Assembly Method :: FALCON v. DX 2.0.1; FALCON-Unzip v. DX 1.2.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano So