The Vertebrate Genomes Project Phase I: A global reference genome resource
Jun 26, 2026·
G Formenti, DE Absolon, LAL Abueg, F Ackerman, FO Al-Ajli, A Aleixo, A Antunes, D Arcila, J-N Audet, JR Balacco, AJS Beavan, K Belov, R Betancur-R, SL Bidwell, MT Biegler, I Bista, M Blaxter, K Boyer, I Braasch, IR Bradbury, N Brajuka, AM Bronikowski, T Brown, G Butler, S Cao, E Charvel, Y Chen, C Ciofi, HM Clawson, JC Collins, S Correard, S Corrigan, M Couture, AJ Crawford, ND D’Alessandre, HB da Conceicao, RR da Fonseca, M Daigavane, J Dalapicolla, M de Bruyn, E de Jong, DN De Panis, HW Detrich III, C DeWeese Scott, M Diekhans, E Duarte, R Durbin, M Escalona, M Eschenbrenner, O Fedrigo, J Fenn, P Flannery, N Forde, SM Gable, PA Galante, R Ganesan, A Gardiner, E Garrison, NJ Gemmell, MTP Gilbert, F Giudicelli, TM Gonçalves, GDA Guardia, A Guarracino, A Gupta, B Haase, D Hays, G Hickey, M Hiller, PM Hime, CJ Hogg, KM Horan, K Howe, D Jackson, N Jain, L Kang, S Kliver, BJ Ko, K-P Koepfli, A Komissarov, LM Komoroske, B Koo, S Koren, J Korlach, I Kovacic, K Krasheninnikova, LF Kuderna, RA Langlois, D Lariviere, DM Larkin, C Lee, YH Lee, HA Lewin, D Lim, RN Lou, SS Mak, KD Makova, L Marín-Gual, T Marques-Bonet, FJ Martin, TC Mathers, CJ Mazzoni, K McCaffrey, SA McCarthy, JA Medico, RLV Mercuri, A Meyer, P Michalak, S Mirarab, PA Morin, J Mountcastle, RW Murphy, TD Murphy, EW Myers, GJ Naylor, T Near, A Nekrutenko, Z Ning, BJ Novak, MF O’Brien, MJ O’Connell, BP O’Toole, S Paez, B Paten, M Paulini, SE Pelan, M Pennell, AR Pfenning, AM Phillippy, B Pinto, M Pippel, M Popova, M Prylutskyi, A Rhie, H Roest Crollius, A Ruiz-Herrera, O Ryder, Y Safonova, CA Santos, MC Schatz, S Secomandi, HB Shaffer, L Shalmiyev, B Shapiro, JJ Smith, M Sollitto, CG Sotero-Caio, CC Steiner, PH Sudmant, DJ Sweeney, SC Talbot, CH Taylor, EC Teeling, F Thibaud-Nissen, T Tilley, N Timoshevskaya, P Traore, Y Turakhia, M Uliano-Silva, C Venditti, B Venkatesh, SC Vernes, WC Warren, CV Whelan, MA Wilson, S Winkler, JM Wood, G Zhang, G Zhao, ED Jarvis, the Vertebrate Genomes Project Consortium Phase I
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Abstract
The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species1. 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 ∼95% of vertebrate orders, along with additional lineages within those orders, totaling 816 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 methods2–4, alongside the growth of associated consortium initiatives and international collaborations5–9. 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 a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.
Type
Publication
bioRxiv
Authors
Postdoctoral Scholar
Currently, Byung June focuses on telomere-to-telomere genome assembly and the functional research of chromatin’s complex structure, particularly in sex chromosomes. Prior to bioinformatics, Byung June majored in conservation genetics, focusing on identifying the genetic diversity and structure of the leopard cat in the South Korea during his M.S. course, supervised by Prof. Soo Hyung Eo. This research sparked his interest in bioinformatics and genome functionality, leading to his false gene gain research collaboration with the Vertebrate Genomes Project during his Ph.D. course at Seoul National University, supervised by Prof. Heebal Kim. Outside of science, Byung June enjoyed playing bass and electric guitar and now enjoys weight lifting and walking in peaceful towns.
Authors
Professor
Kateryna is interested in genomics, evolution, and human genetics.
Her lab studies mutations using both computational and experimental
approaches. Additional topics of interest include sex chromosome
evolution and genomics of childhood obesity.
Authors
Prof. Nekrutenko performed postdoctoral work at the University of Chicago where he found his interest in computational genomics. After moving to the Pennsylvania State University as an Assistant Professor, he and his collaborators developed the Galaxy platform for analysis of biological data. He is now a professor of biochemistry and molecular biology and founding member of galaxyproject.org.
Authors
Dr. Adam Phillippy is a Senior Investigator and head of the Genome Informatics Section at the National Human Genome Research Institute. His lab develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. He is a pioneer of single-molecule sequencing for the reconstruction of complete genomes and is best known for his work on completing the human genome from “telomere to telomere”.
