Vertebrate Genomes Project
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.
|
Acanthopagrus latus
|
GCA_904848185.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Acipenser ruthenus
|
GCA_902713435.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Acipenser ruthenus
|
GCA_902713435.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Acomys russatus
|
GCA_903995435.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Alosa sapidissima
|
GCA_018492685.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Ammodytes marinus
|
GCA_949987685.1
|
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
|
|
Anabas testudineus
|
GCA_900324465.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Anableps anableps
|
GCA_014839685.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Anas platyrhynchos (Pekin duck)
|
GCA_015476345.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Anguilla anguilla
|
GCA_013347855.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Anopheles marshallii
|
GCA_943734725.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Apus apus
|
GCA_020740795.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.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
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Astatotilapia calliptera
|
GCA_900246225.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Astatotilapia calliptera
|
GCA_900246225.5
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Asterias rubens
|
GCA_902459465.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Balaenoptera musculus
|
GCA_009873245.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Balaenoptera musculus
|
GCA_009873245.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Bos indicus x Bos taurus
|
GCA_003369695.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Bos indicus x Bos taurus
|
GCA_003369685.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Callithrix jacchus
|
GCA_011100555.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Calypte anna
|
GCA_003957555.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Carcharodon carcharias
|
GCA_017639515.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Chelmon rostratus
|
GCA_017976325.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Chelonia mydas
|
GCA_015237465.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Chiroxiphia lanceolata
|
GCA_009829145.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Choloepus didactylus
|
GCA_015220235.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Corvus moneduloides
|
GCA_009650955.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
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
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Cygnus olor
|
GCA_009769625.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Denticeps clupeoides
|
GCA_900700375.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Denticeps clupeoides
|
GCA_900700375.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Dromaius novaehollandiae
|
GCA_016128335.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Dryobates pubescens
|
GCA_014839835.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Electrophorus electricus
|
GCA_013358815.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Electrophorus electricus
|
GCA_003665695.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Elephas maximus indicus
|
GCA_024166365.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Esox lucius
|
GCA_004634155.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Esox lucius
|
GCA_011004845.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Falco peregrinus
|
GCA_023634155.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Gadus morhua
|
GCA_902167405.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Gallus gallus
|
GCA_016699485.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Gallus gallus (whiteleghornlayer)
|
GCA_016700215.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
ensembl.org
|
|
Gallus gallus (Cobb)
|
GCA_027408225.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Gallus gallus (Ross)
|
GCA_027557775.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Geothlypis trichas
|
GCA_009764595.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Girardinichthys multiradiatus
|
GCA_021462225.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Gopherus evgoodei
|
GCA_007399415.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Grus americana
|
GCA_028858705.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Haemorhous mexicanus
|
GCA_027477595.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Hippoglossus hippoglossus
|
GCA_009819705.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Hirundo rustica
|
GCA_015227805.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Hyla sarda
|
GCA_029499605.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Jaculus jaculus
|
GCA_020740685.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Lacerta agilis
|
GCA_009819535.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Loxodonta africana
|
GCA_030014295.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.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
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Melanotaenia boesemani
|
GCA_017639745.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Melopsittacus undulatus
|
GCA_012275295.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Mustela erminea
|
GCA_009829155.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Myripristis murdjan
|
GCA_902150065.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Nesoenas mayeri
|
GCA_963082525.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Notolabrus celidotus
|
GCA_009762535.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Notothenia rossii
|
GCA_949606895.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Nycticebus coucang
|
GCA_027406575.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Odontesthes bonariensis
|
GCA_027942865.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Onychomys torridus
|
GCA_903995425.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Pangasianodon hypophthalmus
|
GCA_027358585.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Parambassis ranga
|
GCA_900634625.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Parambassis ranga
|
GCA_900634625.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Petromyzon marinus
|
GCA_010993605.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Phocoena sinus
|
GCA_008692025.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Pholidichthys leucotaenia
|
GCA_020510985.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Phyllostomus discolor
|
GCA_004126475.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Pristis pectinata
|
GCA_009764475.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Pygocentrus nattereri
|
GCA_001682695.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Pygocentrus nattereri
|
GCA_015220715.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Rhinolophus ferrumequinum
|
GCA_004115265.3
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Salarias fasciatus
|
GCA_902148845.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Scatophagus argus
|
GCA_020382885.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Scleropages formosus
|
GCA_900964775.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Sebastes umbrosus
|
GCA_015220745.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Sorex araneus
|
GCA_027595985.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Sphaeramia orbicularis
|
GCA_902148855.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Suncus etruscus
|
GCA_024139225.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Sylvia borin
|
GCA_014839755.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Taeniopygia guttata
|
GCA_008822105.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Tamandua tetradactyla
|
GCA_023851605.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Thalassophryne amazonica
|
GCA_902500255.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Thamnophis elegans
|
GCA_009769535.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Thunnus albacares
|
GCA_914725855.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
–
|
FTP dumps
|
rapid.ensembl.org
|
|
Toxotes jaculatrix
|
GCA_017976425.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Tursiops truncatus
|
GCA_011762595.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|
|
Zalophus californianus
|
GCA_009762305.1
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
ensembl.org
|
|
Zalophus californianus
|
GCA_009762305.2
|
GTF,
GFF3
|
FASTA
|
FASTA
|
FASTA
|
Repeatmodeler
|
FTP dumps
|
rapid.ensembl.org
|