{
  "abstract": "The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ∼97% of vertebrate orders, along with additional lineages within those orders, totaling 815 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods, alongside the growth of associated consortium initiatives and international collaborations. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers the reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.",
  "abstract_shown": true,
  "affiliations": [
    "Vertebrate Genome Laboratory, The Rockefeller University;",
    "Tree of Life, Wellcome Sanger Institute;",
    "Katara Biodiversity Genomes Program;",
    "Vale Institute of Technology;",
    "CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto;",
    "Scripps Institution of Oceanography, University of California San Diego;",
    "Rockefeller University Field Research Center;",
    "Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester;",
    "School of Life and Environmental Sciences, The University of Sydney;",
    "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health;",
    "Laboratory of Neurogenetics of Language, The Rockefeller University;",
    "Senckenberg Research Institute and Natural History Museum;",
    "Washington University School of Medicine;",
    "Department of Integrative Biology, Michigan State University;",
    "Fisheries and Oceans Canada;",
    "Dept of Ecology, Evolution, Organismal Biology, Iowa State University;",
    "Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG);",
    "University College London Cancer Institute, University College London;",
    "Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center;",
    "Bioinformatics and Systems Biology Graduate Program, UC San Diego;",
    "Department of Biology, University of Florence;",
    "UC Santa Cruz Genomics Institute;",
    "GenOuest, Univ Rennes, INRIA, CNRS, IRISA;",
    "Minderoo OceanOmics Centre at UWA, UWA Oceans Institute, The University of Western Australia;",
    "Departamento de Ciencias Biologicas, Universidad de los Andes;",
    "Centro de Oncologia Molecular, Hospital Sirio-Libanes;",
    "Boston Children's Hospital;",
    "Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen;",
    "Yale University;",
    "Departamento de Sistematica e Ecologia, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraiba;",
    "Australian Research Centre for Human Evolution, Griffith University;",
    "Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW);",
    "Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University;",
    "Institute for Systems Genomics, University of Connecticut;",
    "Center for Reproductive Health, School of Regeneration and Repair, University of Edinburgh;",
    "Global Futures Laboratory, Arizona State University;",
    "Ray and Stephanie Lane Department of Computational Biology, School of Computer Science, Carnegie Mellon University;",
    "Department of Genetics, University of Cambridge;",
    "Department of Anatomy, Faculty of Biomedical Sciences, University of Otago;",
    "Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen;"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 100,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Giulio Formenti",
      "orcid": "0000-0002-7554-5991"
    },
    {
      "affs": [
        1
      ],
      "name": "Dominic E. Absolon",
      "orcid": "0009-0004-5709-2249"
    },
    {
      "affs": [
        0
      ],
      "name": "Linelle Ann L. Abueg",
      "orcid": "0000-0002-6879-3954"
    },
    {
      "affs": [
        0
      ],
      "name": "Francine Ackerman",
      "orcid": "0009-0009-5957-829X"
    },
    {
      "affs": [
        2
      ],
      "name": "Farooq O. Al-Ajli",
      "orcid": "0000-0002-4692-7106"
    },
    {
      "affs": [
        3
      ],
      "name": "Alexandre Luis Padovan Aleixo",
      "orcid": "0000-0002-7816-9725"
    },
    {
      "affs": [
        4
      ],
      "name": "Agostinho Antunes",
      "orcid": "0000-0002-1328-1732"
    },
    {
      "affs": [
        5
      ],
      "name": "Dahiana Arcila",
      "orcid": "0000-0002-5126-1345"
    },
    {
      "affs": [
        6
      ],
      "name": "Jean‐Nicolas Audet",
      "orcid": "0000-0002-0511-183X"
    },
    {
      "affs": [
        0
      ],
      "name": "Jennifer Balacco",
      "orcid": "0000-0001-7102-1632"
    },
    {
      "affs": [
        7
      ],
      "name": "Alan J. S. Beavan",
      "orcid": "0000-0002-8219-6742"
    },
    {
      "affs": [
        8
      ],
      "name": "Katherine Belov",
      "orcid": "0000-0002-9762-5554"
    },
    {
      "affs": [
        5
      ],
      "name": "Ricardo Betancur‐R",
      "orcid": "0000-0002-9512-5011"
    },
    {
      "affs": [
        9
      ],
      "name": "Shelby L. Bidwell"
    },
    {
      "affs": [
        10
      ],
      "name": "Matthew T. Biegler",
      "orcid": "0000-0003-4331-9890"
    },
    {
      "affs": [
        11
      ],
      "name": "Iliana Bista",
      "orcid": "0000-0002-6155-3093"
    },
    {
      "affs": [
        1
      ],
      "name": "Mark Blaxter",
      "orcid": "0000-0003-2861-949X"
    },
    {
      "affs": [
        12
      ],
      "name": "Kevin Boyer"
    },
    {
      "affs": [
        13
      ],
      "name": "Ingo Braasch",
      "orcid": "0000-0003-4766-611X"
    },
    {
      "affs": [
        14
      ],
      "name": "Ian Bradbury",
      "orcid": "0000-0002-8152-4943"
    },
    {
      "affs": [
        0
      ],
      "name": "Nadolina Brajuka",
      "orcid": "0009-0008-6639-8791"
    },
    {
      "affs": [
        15
      ],
      "name": "Anne M. Bronikowski",
      "orcid": "0000-0001-6432-298X"
    },
    {
      "affs": [
        16
      ],
      "name": "Tom Brown",
      "orcid": "0000-0001-8293-4816"
    },
    {
      "affs": [
        17
      ],
      "name": "George B. Butler",
      "orcid": "0000-0002-6207-6225"
    },
    {
      "affs": [
        18
      ],
      "name": "Shuo Cao"
    },
    {
      "affs": [
        19
      ],
      "name": "Eduardo Charvel",
      "orcid": "0000-0001-8583-8491"
    },
    {
      "affs": [
        0
      ],
      "name": "Ying Chen",
      "orcid": "0000-0002-2237-6426"
    },
    {
      "affs": [
        20
      ],
      "name": "Claúdio Ciofi",
      "orcid": "0000-0001-8537-8659"
    },
    {
      "affs": [
        21
      ],
      "name": "Hiram Clawson",
      "orcid": "0000-0002-0480-0545"
    },
    {
      "affs": [
        1
      ],
      "name": "Joanna Collins",
      "orcid": "0000-0001-5782-5028"
    },
    {
      "affs": [
        22
      ],
      "name": "Solenne Correard",
      "orcid": "0000-0002-0554-5443"
    },
    {
      "affs": [
        23
      ],
      "name": "Shannon L. Corrigan",
      "orcid": "0000-0003-0093-5028"
    },
    {
      "affs": [
        0
      ],
      "name": "Mélanie Couture",
      "orcid": "0000-0002-6169-8225"
    },
    {
      "affs": [
        24
      ],
      "name": "Andrew J. Crawford",
      "orcid": "0000-0003-3153-6898"
    },
    {
      "affs": [
        25
      ],
      "name": "Nathália Da Roz D’Alessandre",
      "orcid": "0009-0001-7332-0182"
    },
    {
      "affs": [
        26
      ],
      "name": "Helena B. Conceição",
      "orcid": "0000-0003-3876-5407"
    },
    {
      "affs": [
        27
      ],
      "name": "Rute R. da Fonseca",
      "orcid": "0000-0002-2805-4698"
    },
    {
      "affs": [
        28
      ],
      "name": "Minoli Daigavane"
    },
    {
      "affs": [
        29
      ],
      "name": "Jeronymo Dalapicolla",
      "orcid": "0000-0002-4819-9720"
    },
    {
      "affs": [
        30
      ],
      "name": "Mark de Bruyn",
      "orcid": "0000-0003-1528-9604"
    },
    {
      "affs": [
        23
      ],
      "name": "Emma de Jong",
      "orcid": "0000-0002-2501-6119"
    },
    {
      "affs": [
        31
      ],
      "name": "Diego N. De Panis",
      "orcid": "0000-0002-3679-9585"
    },
    {
      "affs": [
        32
      ],
      "name": "H. William Detrich",
      "orcid": "0000-0002-0783-4505"
    },
    {
      "affs": [
        9
      ],
      "name": "C Scott",
      "orcid": "0009-0007-3455-7447"
    },
    {
      "affs": [
        21
      ],
      "name": "Mark Diekhans",
      "orcid": "0000-0002-0430-0989"
    },
    {
      "affs": [
        0
      ],
      "name": "Erick Duarte",
      "orcid": "0009-0009-1100-6583"
    },
    {
      "affs": [
        1
      ],
      "name": "Richard Michael Durbin",
      "orcid": "0000-0002-9130-1006"
    },
    {
      "affs": [
        33
      ],
      "name": "Merly Escalona",
      "orcid": "0000-0003-0213-4777"
    },
    {
      "affs": [
        9
      ],
      "name": "Michel Eschenbrenner"
    },
    {
      "affs": [
        0
      ],
      "name": "Olivier D. Fedrigo",
      "orcid": "0000-0002-6450-7551"
    },
    {
      "affs": [
        7
      ],
      "name": "Jonathan Fenn",
      "orcid": "0000-0002-9255-6975"
    },
    {
      "affs": [
        0
      ],
      "name": "Patrick C. Flannery",
      "orcid": "0009-0008-4343-4198"
    },
    {
      "affs": [
        34
      ],
      "name": "Niamh Forde",
      "orcid": "0000-0002-3539-9643"
    },
    {
      "affs": [
        35
      ],
      "name": "Simone M. Gable",
      "orcid": "0000-0001-6656-4034"
    },
    {
      "affs": [
        25
      ],
      "name": "Pedro A. F. Galante",
      "orcid": "0000-0002-4820-4155"
    },
    {
      "affs": [
        36
      ],
      "name": "Rajee Ganesan",
      "orcid": "0000-0003-3020-8729"
    },
    {
      "affs": [
        37
      ],
      "name": "Amanda M. Gardiner",
      "orcid": "0009-0002-5518-1235"
    },
    {
      "affs": [
        18
      ],
      "name": "Erik P. Garrison",
      "orcid": "0000-0003-3821-631X"
    },
    {
      "affs": [
        38
      ],
      "name": "Neil J. Gemmell",
      "orcid": "0000-0003-0671-3637"
    },
    {
      "affs": [
        39
      ],
      "name": "Marcus Thomas P. Gilbert",
      "orcid": "0000-0002-5805-7195"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ajm8n5vkgzgv1.bib",
  "cited_by": 24,
  "doi": "10.64898/2026.06.24.732306",
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  "id": "ajm8n5vkgzgv1",
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  "landing_url": "https://hal.science/hal-05785854v1",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
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      "1312|Genomics and Phylogenetic Studies"
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  "pdf_url": "https://www.biorxiv.org/content/biorxiv/early/2026/06/26/2026.06.24.732306.full.pdf",
  "pmcid": "PMC13320880",
  "pmid": "42395566",
  "published": "2026-06-26",
  "publisher": "Cold Spring Harbor Laboratory",
  "ris": "https://research.draconitic.com/paper/ajm8n5vkgzgv1.ris",
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      "first_seen": "2026-10-30T12:17:50Z",
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      "url": "https://hal.science/hal-05785854v1"
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  "subjects": [
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      "subfield": "proteomics-metabolomics"
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      "field": "biology",
      "origin": "hal:0.sdv",
      "subfield": "general"
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  ],
  "title": "The Vertebrate Genomes Project Phase I: A global reference genome resource",
  "title_text": "The Vertebrate Genomes Project Phase I: A global reference genome resource",
  "type": "preprint",
  "updated_at": "2026-11-09T13:21:05Z",
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