AUTHOR=Morin Phillip A. , Bein Bernhard , Bortoluzzi Chiara , Bukhman Yury V. , Hains Taylor , Heimeier Dorothea , Uliano-Silva Marcela , Absolon Dominic E. , Abueg Linelle , Antosiewicz-Bourget Jessica , Balacco Jennifer R. , Bonde Robert K. , Brajuka Nadolina , Brownlow Andrew C. , Carroll Emma L. , Carter Molly , Collins Joanna , Davison Nicholas J. , Denton Amy , Fedrigo Olivier , Foote Andrew D. , Formenti Giulio , Gallo Guido R. , Greve Carola , Houck Marlys L. , Howard Caroline , Jacobsen Jeff K. , Jain Nivesh , Krasheninnikova Ksenia , Maloney Brigid M. , Manley Bethan F. , Mathers Thomas C. , Mccarthy Shane A. , Mcgowen Michael R. , Meyer Susanne , Mountcastle Jacquelyn , Neely Benjamin A. , O’toole Brian , Pelan Sarah , Rosel Patricia E. , Rowles Teri K. , Ryder Oliver A. , Schell Tilman , Sims Ying , St Leger Judy , Stewart Ron , Ternes Kerstin , Tilley Tatiana , Whelan Conor , Wood Jonathan M. D. , Hiller Michael , Blaxter Mark , Jarvis Erich D. 

TITLE=Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life

JOURNAL=Frontiers in Marine Science

VOLUME=Volume 12 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2025.1562045

DOI=10.3389/fmars.2025.1562045

ISSN=2296-7745

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. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) 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, 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 have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.