Vertebrate Genomes Project

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The Vertebrate Genomes Project (VGP) aims to generate near error-free reference genome assemblies of ~70,000 extant vertebrate species. These genomes will be used to address fundamental questions in biology and disease, to identify species most genetically at risk for extinction, and to preserve genetic information of life.

The VGP will be completed in four phases based on taxonomic hierarchy: a representative of each order (phase 1), followed by each family (phase 2), followed by each genus (phase 3), finally followed by all species (phase 4).

Ensembl is a partner in the VGP and we annotate the protein-coding and non-coding RNA gene structures using a re-engineered version of our Gene Annotation System (Aken et al, 2017). After QC, genomes and annotations are made available via our FTP site (see table below) before subsequently being made available in the Ensembl Genome Browser.

Image Species Accession Annotation Proteins Transcripts Softmasked genome Repeat library Other data View in browser
Acipenser ruthenus GCA_902713435.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Amblyraja radiata GCA_010909765.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Anabas testudineus GCA_900324465.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Anabas testudineus GCA_900324465.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps rapid.ensembl.org
Anguilla anguilla GCA_013347855.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Aquila chrysaetos chrysaetos GCA_900496995.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Archocentrus centrarchus GCA_007364275.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps rapid.ensembl.org
Arvicanthis niloticus GCA_011762505.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Astatotilapia calliptera GCA_900246225.3 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Balaenoptera musculus GCA_009873245.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Balaenoptera musculus GCA_009873245.3 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Betta splendens GCA_900634795.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Callithrix jacchus GCA_011100555.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Catharus ustulatus GCA_009819885.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Chiroxiphia lanceolata GCA_009829145.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Choloepus didactylus GCA_015220235.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Corvus moneduloides GCA_009650955.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Cottoperca gobio GCA_900634415.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Cyclopterus lumpus GCA_009769545.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Denticeps clupeoides GCA_900700375.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Denticeps clupeoides GCA_900700375.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Echeneis naucrates GCA_900963305.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Electrophorus electricus GCA_013358815.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Erpetoichthys calabaricus GCA_900747795.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Gadus morhua GCA_902167405.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Gopherus evgoodei GCA_007399415.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Gouania willdenowi GCA_900634775.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Gymnodraco acuticeps GCA_902827175.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Harpagifer antarcticus GCA_902827135.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Hirundo rustica GCA_015227805.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Lacerta agilis GCA_009819535.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Lynx canadensis GCA_007474595.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Mastacembelus armatus GCA_900324485.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Mastacembelus armatus GCA_900324485.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps rapid.ensembl.org
Megalops cyprinoides GCA_013368585.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Melopsittacus undulatus GCA_012275295.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Myripristis murdjan GCA_902150065.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Notolabrus celidotus GCA_009762535.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Ornithorhynchus anatinus GCA_004115215.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Parambassis ranga GCA_900634625.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Periophthalmus magnuspinnatus GCA_009829125.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Phocoena sinus GCA_008692025.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Phyllostomus discolor GCA_004126475.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps rapid.ensembl.org
Pseudochaenichthys georgianus GCA_902827115.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Pygocentrus nattereri GCA_015220715.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Rattus norvegicus (BN/NHsdMcwi) GCA_015227675.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Salarias fasciatus GCA_902148845.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Salmo trutta GCA_901001165.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Sarcophilus harrisii GCA_902635505.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Sciurus vulgaris GCA_902686455.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Scleropages formosus GCA_900964775.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Sparus aurata GCA_900880675.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Sphaeramia orbicularis GCA_902148855.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Strigops habroptila GCA_004027225.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Taeniopygia guttata GCA_008822105.1 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps rapid.ensembl.org
Taeniopygia guttata GCA_003957565.2 GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Takifugu rubripes GCA_901000725.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Thalassophryne amazonica GCA_902500255.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Thamnophis elegans GCA_009769535.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Trematomus bernacchii GCA_902827165.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Tursiops truncatus GCA_011762595.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Zalophus californianus GCA_009762305.1 GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Zalophus californianus GCA_009762305.2 GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org