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

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

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. Tow...

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Main Authors: Phillip A. Morin, Bernhard Bein, Chiara Bortoluzzi, Yury V. Bukhman, Taylor Hains, Dorothea Heimeier, Marcela Uliano-Silva, Dominic E. Absolon, Linelle Abueg, Jessica Antosiewicz-Bourget, Jennifer R. Balacco, Robert K. Bonde, Nadolina Brajuka, Andrew C. Brownlow, Emma L. Carroll, Molly Carter, Joanna Collins, Nicholas J. Davison, Amy Denton, Olivier Fedrigo, Andrew D. Foote, Giulio Formenti, Guido R. Gallo, Carola Greve, Marlys L. Houck, Caroline Howard, Jeff K. Jacobsen, Nivesh Jain, Ksenia Krasheninnikova, Brigid M. Maloney, Bethan F. Manley, Thomas C. Mathers, Shane A. Mccarthy, Michael R. Mcgowen, Susanne Meyer, Jacquelyn Mountcastle, Benjamin A. Neely, Brian O’toole, Sarah Pelan, Patricia E. Rosel, Teri K. Rowles, Oliver A. Ryder, Tilman Schell, Ying Sims, Judy St Leger, Ron Stewart, Kerstin Ternes, Tatiana Tilley, Conor Whelan, Jonathan M. D. Wood, Michael Hiller, Mark Blaxter, Erich D. Jarvis
Format: Article
Language:English
Published: Frontiers Media S.A. 2025-07-01
Series:Frontiers in Marine Science
Subjects:
reference genome
comparative genomics
conservation genomics
whale
dolphin
porpoise
Online Access:https://www.frontiersin.org/articles/10.3389/fmars.2025.1562045/full
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Summary: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.
ISSN:2296-7745

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