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The Vertebrate Genomes Project Phase I: A global reference genome resource
40 affiliations
- 1Vertebrate Genome Laboratory, The Rockefeller University;
- 2Tree of Life, Wellcome Sanger Institute;
- 3Katara Biodiversity Genomes Program;
- 4Vale Institute of Technology;
- 5CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto;
- 6Scripps Institution of Oceanography, University of California San Diego;
- 7Rockefeller University Field Research Center;
- 8Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester;
- 9School of Life and Environmental Sciences, The University of Sydney;
- 10National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health;
- 11Laboratory of Neurogenetics of Language, The Rockefeller University;
- 12Senckenberg Research Institute and Natural History Museum;
- 13Washington University School of Medicine;
- 14Department of Integrative Biology, Michigan State University;
- 15Fisheries and Oceans Canada;
- 16Dept of Ecology, Evolution, Organismal Biology, Iowa State University;
- 17Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG);
- 18University College London Cancer Institute, University College London;
- 19Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center;
- 20Bioinformatics and Systems Biology Graduate Program, UC San Diego;
- 21Department of Biology, University of Florence;
- 22UC Santa Cruz Genomics Institute;
- 23GenOuest, Univ Rennes, INRIA, CNRS, IRISA;
- 24Minderoo OceanOmics Centre at UWA, UWA Oceans Institute, The University of Western Australia;
- 25Departamento de Ciencias Biologicas, Universidad de los Andes;
- 26Centro de Oncologia Molecular, Hospital Sirio-Libanes;
- 27Boston Children's Hospital;
- 28Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen;
- 29Yale University;
- 30Departamento de Sistematica e Ecologia, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraiba;
- 31Australian Research Centre for Human Evolution, Griffith University;
- 32Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW);
- 33Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University;
- 34Institute for Systems Genomics, University of Connecticut;
- 35Center for Reproductive Health, School of Regeneration and Repair, University of Edinburgh;
- 36Global Futures Laboratory, Arizona State University;
- 37Ray and Stephanie Lane Department of Computational Biology, School of Computer Science, Carnegie Mellon University;
- 38Department of Genetics, University of Cambridge;
- 39Department of Anatomy, Faculty of Biomedical Sciences, University of Otago;
- 40Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen;
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.
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BibTeX
@misc{formenti2026vertebrate,
title = {{The Vertebrate Genomes Project Phase I: A global reference genome resource}},
author = {Giulio Formenti and Dominic E. Absolon and Linelle Ann L. Abueg and Francine Ackerman and Farooq O. Al-Ajli and Alexandre Luis Padovan Aleixo and Agostinho Antunes and Dahiana Arcila and Jean‐Nicolas Audet and Jennifer Balacco and Alan J. S. Beavan and Katherine Belov and Ricardo Betancur‐R and Shelby L. Bidwell and Matthew T. Biegler and Iliana Bista and Mark Blaxter and Kevin Boyer and Ingo Braasch and Ian Bradbury and Nadolina Brajuka and Anne M. Bronikowski and Tom Brown and George B. Butler and Shuo Cao and Eduardo Charvel and Ying Chen and Claúdio Ciofi and Hiram Clawson and Joanna Collins and Solenne Correard and Shannon L. Corrigan and Mélanie Couture and Andrew J. Crawford and Nathália Da Roz D’Alessandre and Helena B. Conceição and Rute R. da Fonseca and Minoli Daigavane and Jeronymo Dalapicolla and Mark de Bruyn and Emma de Jong and Diego N. De Panis and H. William Detrich and C Scott and Mark Diekhans and Erick Duarte and Richard Michael Durbin and Merly Escalona and Michel Eschenbrenner and Olivier D. Fedrigo and Jonathan Fenn and Patrick C. Flannery and Niamh Forde and Simone M. Gable and Pedro A. F. Galante and Rajee Ganesan and Amanda M. Gardiner and Erik P. Garrison and Neil J. Gemmell and Marcus Thomas P. Gilbert},
howpublished = {HAL},
year = {2026},
month = jun,
doi = {10.64898/2026.06.24.732306},
url = {https://hal.science/hal-05785854v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - The Vertebrate Genomes Project Phase I: A global reference genome resource
AU - Giulio Formenti
AU - Dominic E. Absolon
AU - Linelle Ann L. Abueg
AU - Francine Ackerman
AU - Farooq O. Al-Ajli
AU - Alexandre Luis Padovan Aleixo
AU - Agostinho Antunes
AU - Dahiana Arcila
AU - Jean‐Nicolas Audet
AU - Jennifer Balacco
AU - Alan J. S. Beavan
AU - Katherine Belov
AU - Ricardo Betancur‐R
AU - Shelby L. Bidwell
AU - Matthew T. Biegler
AU - Iliana Bista
AU - Mark Blaxter
AU - Kevin Boyer
AU - Ingo Braasch
AU - Ian Bradbury
AU - Nadolina Brajuka
AU - Anne M. Bronikowski
AU - Tom Brown
AU - George B. Butler
AU - Shuo Cao
AU - Eduardo Charvel
AU - Ying Chen
AU - Claúdio Ciofi
AU - Hiram Clawson
AU - Joanna Collins
AU - Solenne Correard
AU - Shannon L. Corrigan
AU - Mélanie Couture
AU - Andrew J. Crawford
AU - Nathália Da Roz D’Alessandre
AU - Helena B. Conceição
AU - Rute R. da Fonseca
AU - Minoli Daigavane
AU - Jeronymo Dalapicolla
AU - Mark de Bruyn
AU - Emma de Jong
AU - Diego N. De Panis
AU - H. William Detrich
AU - C Scott
AU - Mark Diekhans
AU - Erick Duarte
AU - Richard Michael Durbin
AU - Merly Escalona
AU - Michel Eschenbrenner
AU - Olivier D. Fedrigo
AU - Jonathan Fenn
AU - Patrick C. Flannery
AU - Niamh Forde
AU - Simone M. Gable
AU - Pedro A. F. Galante
AU - Rajee Ganesan
AU - Amanda M. Gardiner
AU - Erik P. Garrison
AU - Neil J. Gemmell
AU - Marcus Thomas P. Gilbert
PY - 2026
DA - 2026/06/26
PB - HAL
DO - 10.64898/2026.06.24.732306
UR - https://hal.science/hal-05785854v1
AB - 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.
ER -