Frontiers in Marine Science (Jul 2025)
Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life
- Phillip A. Morin,
- Bernhard Bein,
- Bernhard Bein,
- Chiara Bortoluzzi,
- Yury V. Bukhman,
- Taylor Hains,
- Taylor Hains,
- Dorothea Heimeier,
- Marcela Uliano-Silva,
- 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,
- Michael Hiller,
- Mark Blaxter,
- Erich D. Jarvis,
- Erich D. Jarvis
Affiliations
- Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
- Bernhard Bein
- LOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, Germany
- Bernhard Bein
- Institute of Cell Biology & Neuroscience, Faculty of Biological Sciences, Goethe University, Frankfurt, Germany
- Chiara Bortoluzzi
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Yury V. Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
- Taylor Hains
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, United States
- Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States
- Dorothea Heimeier
- School of Biological Sciences, The University of Auckland–Waipapa Taumata Rau, Auckland, Aotearoa, New Zealand
- Marcela Uliano-Silva
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Marcela Uliano-Silva
- Faculty of Life Sciences and Aquaculture, Nord University, Bodø, Norway
- Dominic E. Absolon
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Linelle Abueg
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Jessica Antosiewicz-Bourget
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
- Jennifer R. Balacco
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Robert K. Bonde
- 1Wetland and Aquatic Research Center, U.S. Geological Survey (USGS), Gainesville, FL, United States
- Nadolina Brajuka
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Andrew C. Brownlow
- 2School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Emma L. Carroll
- School of Biological Sciences, The University of Auckland–Waipapa Taumata Rau, Auckland, Aotearoa, New Zealand
- Molly Carter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Nicholas J. Davison
- 2School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Amy Denton
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Olivier Fedrigo
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Andrew D. Foote
- 3Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Giulio Formenti
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Guido R. Gallo
- 4Department of Biosciences, University of Milan, Milan, Italy
- Carola Greve
- LOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, Germany
- Marlys L. Houck
- 5Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
- Caroline Howard
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Jeff K. Jacobsen
- 6V.E. Enterprises, Arcada, CA, United States
- Nivesh Jain
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Ksenia Krasheninnikova
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Brigid M. Maloney
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Bethan F. Manley
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Thomas C. Mathers
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Shane A. Mccarthy
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Michael R. Mcgowen
- 7Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Susanne Meyer
- 8Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Jacquelyn Mountcastle
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Benjamin A. Neely
- 9National Institute of Standards and Technology, Charleston, NC, United States
- Brian O’toole
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Patricia E. Rosel
- 0Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Lafayette, LA, United States
- Teri K. Rowles
- 1Office of Protected Resources, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, MD, United States
- Oliver A. Ryder
- 5Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
- Tilman Schell
- LOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, Germany
- Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Judy St Leger
- 2New York State College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
- Kerstin Ternes
- 3Zoo Duisburg AG, Duisburg, Germany
- Tatiana Tilley
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Conor Whelan
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Jonathan M. D. Wood
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Michael Hiller
- LOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, Germany
- Michael Hiller
- Institute of Cell Biology & Neuroscience, Faculty of Biological Sciences, Goethe University, Frankfurt, Germany
- Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
- Erich D. Jarvis
- 0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Erich D. Jarvis
- 4Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, United States
- DOI
- https://doi.org/10.3389/fmars.2025.1562045
- Journal volume & issue
-
Vol. 12
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.
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