Genomic infrastructure for cetacean research and conservation: Reference genomes for eight families spanning the cetacean phylogeny

Published

July 2, 2025

Author(s)

Phillip A Morin, Bernhard Bein, Chiara Bortoluzzi, Yury V Bukhman, Taylor Hains, Dorothea Heimeier, Marcela Uliano-Silva, Dominic Absalon, Linelle Abueg, Jessica Antosiewicz-Bourget, Robin W Baird, Jennifer R Balacco, Robert K Bonde, Nadolina Brajuka, Andrew Brownlow, Emma Carroll, Molly Carter, Joanna Collins, Nick Davison, Amy Denton, Olga Dudchenko, Olivier Fedrigo, Giulio Formenti, Andy Foote, Guido Gallo, Carola Greve, Marlys Houck, Caroline Howard, Jeff K Jacobsen, Nivesh Jain, Ksenia Krasheninnikova, Erez Lieberman-Aiden, Brigid Maloney, Bethan Manley, Tom Mathers, Shane McCarthy, Michael McGowen, Susanne Meyer, Jacquelyn Mountcastle, Benjamin Neely, Brian O'Toole, Sarah Pelan, Patricia E Rosel, Teri K Rowles, Oliver A Ryder, Tillman Schell, Ying Sims, Judy St. Leger, Ron Stewart, Kerstin Ternes, James A Thomson, Tatiana Tilley, Conor Whelan, Jo Wood, Michael Hiller, Mark Blaxter, Erich D Jarvis

Abstract

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species, following the methods, goals and genome assembly quality standards set out by the Vertebrate Genomes Project (VGP). To reach that goal, we have generated 13 new reference genomes across eight of the 14 cetacean families, and summarize the genome assembly characteristics for 18 species, including additional published genome assemblies that meet the completeness and quality standards. We predicted ancestral linkage groups for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation of the genomes, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

Citation

Frontiers in Marine Science

Volume

12

Pub Type

Journals

Download Paper

https://doi.org/10.3389/fmars.2025.1562045

Local Download

Keywords

Reference genome, Comparative genomics, Conservation genomics, Whale, dolphin, porpoise, Cetacea

Citation

Morin, P. , Bein, B. , Bortoluzzi, C. , Bukhman, Y. , Hains, T. , Heimeier, D. , Uliano-Silva, M. , Absalon, D. , Abueg, L. , Antosiewicz-Bourget, J. , Baird, R. , Balacco, J. , Bonde, R. , Brajuka, N. , Brownlow, A. , Carroll, E. , Carter, M. , Collins, J. , Davison, N. , Denton, A. , Dudchenko, O. , Fedrigo, O. , Formenti, G. , Foote, A. , Gallo, G. , Greve, C. , Houck, M. , Howard, C. , Jacobsen, J. , Jain, N. , Krasheninnikova, K. , Lieberman-Aiden, E. , Maloney, B. , Manley, B. , Mathers, T. , McCarthy, S. , McGowen, M. , Meyer, S. , Mountcastle, J. , Neely, B. , O'Toole, B. , Pelan, S. , Rosel, P. , Rowles, T. , Ryder, O. , Schell, T. , Sims, Y. , St. Leger, J. , Stewart, R. , Ternes, K. , Thomson, J. , Tilley, T. , Whelan, C. , Wood, J. , Hiller, M. , Blaxter, M. and Jarvis, E. (2025), Genomic infrastructure for cetacean research and conservation: Reference genomes for eight families spanning the cetacean phylogeny, Frontiers in Marine Science, [online], https://doi.org/10.3389/fmars.2025.1562045, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=959259 (Accessed August 9, 2025)