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bioRxiv · 10.64898/2026.06.24.732306

The Vertebrate Genomes Project Phase I: A global reference genome resource

Formenti, G.·Absolon, D. E.·Abueg, L. A. L.·Ackerman, F.·Al-Ajli, F. O.·Aleixo, A.·Antunes, A.·Arcila, D.·Audet, J.-N.·Balacco, J. R.·Beavan, A. J. S.·Belov, K.·Betancur-R., R.·Bidwell, S. L.·Biegler, M. T.·Bista, I.·Blaxter, M.·Boyer, K.·Braasch, I.·Bradbury, I. R.·Brajuka, N.·Bronikowski, A. M.·Brown, T.·Butler, G.·Cao, S.·Charvel, E.·Chen, Y.·Ciofi, C.·Clawson, H. M.·Collins, J. C.·Correard, S.·Corrigan, S.·Couture, M.·Crawford, A. J.·D'Alessandre, N. D. R.·da Conceicao, H. B.·da Fonseca, R. R.·Daigavane, M.·Dalapicolla, J.·de Bruyn, M.·de Jong, E.·D
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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. Talking pointsO_LIThe flagship paper of VGP Phase I C_LIO_LIThe highest quality collection of genomes within the eukaryotic domain of life C_LIO_LIEvolution of genome sequencing technology quality throughout VGP Phase I C_LIO_LIA driver project that has been a model for multiple large-scale, high-quality reference genome projects C_LIO_LIReleases all currently unpublished genomes in Phase I from scientific study embargoes C_LIO_LIMultiple biological discoveries across the vertebrate tree of life C_LI

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Formenti, G., Absolon, D. E., Abueg, L. A. L., Ackerman, F., Al-Ajli, F. O., Aleixo, A., Antunes, A., Arcila, D., Audet, J.-N., Balacco, J. R., Beavan, A. J. S., Belov, K., Betancur-R., R., Bidwell, S. L., Biegler, M. T., Bista, I., Blaxter, M., Boyer, K., Braasch, I., Bradbury, I. R., Brajuka, N., Bronikowski, A. M., Brown, T., Butler, G., Cao, S., Charvel, E., Chen, Y., Ciofi, C., Clawson, H. M., Collins, J. C., Correard, S., Corrigan, S., Couture, M., Crawford, A. J., D'Alessandre, N. D. R., da Conceicao, H. B., da Fonseca, R. R., Daigavane, M., Dalapicolla, J., de Bruyn, M., de Jong, E., D. 2026-06-26. The Vertebrate Genomes Project Phase I: A global reference genome resource. https://doi.org/10.64898/2026.06.24.732306

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