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

作者：Phillip A. Morin, Bernhard Bein, Chiara Bortoluzzi, Yury V. Bukhman, Taylor Hains, Dorothea Heimeier, Marcela Uliano‐Silva, Dominic Absolon, Linelle Abueg, Jessica Antosiewicz‐Bourget, Jennifer Balacco, Robert K. Bonde, Nadolina Brajuka, Andrew Brownlow, Emma L. Carroll, M.T. Carter, Joanna Collins, Nicholas J. Davison, Amy Denton, Olivier Fédrigo, Andrew D. Foote, Giulio Formenti, Guido Roberto Gallo, Carola Greve, Marlys L. Houck, Caroline Howard, Jeff K. Jacobsen, Nivesh Jain, Ksenia Krasheninnikova, Brigid Maloney, Bethan F. Manley, Thomas C. Mathers, Shane McCarthy, Michael R. McGowen, Susanne Meyer, Jacquelyn Mountcastle, Benjamin A. Neely, Brian I. O’Toole, Sarah Pelan, Patricia E. Rosel, Teri Rowles, Oliver A. Ryder, Tilman Schell, Ying Sims, Judy St. Leger, Ron Stewart, Kerstin Ternes, Tatiana Tilley, Conor Whelan, Jonathan Wood, Michael Hiller, Mark Blaxter, Erich D. Jarvis · 发表于：Frontiers in Marine Science · 年份：2025 · DOI：10.3389/fmars.2025.1562045 · 被引用次数：6 · 研究领域：Marine animal studies overview、Identification and Quantification in Food、Environmental DNA in Biodiversity Studies

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 gen...