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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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2025.1562045/full |
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| author | 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 |
| author_facet | 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 |
| author_sort | Phillip A. Morin |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-dae921b7346847619bdfe502e949283f |
| institution | DOAJ |
| issn | 2296-7745 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj-art-dae921b7346847619bdfe502e949283f2025-08-20T02:43:58ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452025-07-011210.3389/fmars.2025.15620451562045Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of lifePhillip A. Morin0Bernhard Bein1Bernhard Bein2Chiara Bortoluzzi3Yury V. Bukhman4Taylor Hains5Taylor Hains6Dorothea Heimeier7Marcela Uliano-Silva8Marcela Uliano-Silva9Dominic E. Absolon10Linelle Abueg11Jessica Antosiewicz-Bourget12Jennifer R. Balacco13Robert K. Bonde14Nadolina Brajuka15Andrew C. Brownlow16Emma L. Carroll17Molly Carter18Joanna Collins19Nicholas J. Davison20Amy Denton21Olivier Fedrigo22Andrew D. Foote23Giulio Formenti24Guido R. Gallo25Carola Greve26Marlys L. Houck27Caroline Howard28Jeff K. Jacobsen29Nivesh Jain30Ksenia Krasheninnikova31Brigid M. Maloney32Bethan F. Manley33Thomas C. Mathers34Shane A. Mccarthy35Michael R. Mcgowen36Susanne Meyer37Jacquelyn Mountcastle38Benjamin A. Neely39Brian O’toole40Sarah Pelan41Patricia E. Rosel42Teri K. Rowles43Oliver A. Ryder44Tilman Schell45Ying Sims46Judy St Leger47Ron Stewart48Kerstin Ternes49Tatiana Tilley50Conor Whelan51Jonathan M. D. Wood52Michael Hiller53Michael Hiller54Mark Blaxter55Erich D. Jarvis56Erich D. Jarvis57Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United StatesLOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, GermanyInstitute of Cell Biology & Neuroscience, Faculty of Biological Sciences, Goethe University, Frankfurt, GermanyTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomRegenerative Biology, Morgridge Institute for Research, Madison, WI, United StatesCommittee on Evolutionary Biology, The University of Chicago, Chicago, IL, United StatesNegaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, United StatesSchool of Biological Sciences, The University of Auckland–Waipapa Taumata Rau, Auckland, Aotearoa, New ZealandTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomFaculty of Life Sciences and Aquaculture, Nord University, Bodø, NorwayTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United StatesRegenerative Biology, Morgridge Institute for Research, Madison, WI, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States1Wetland and Aquatic Research Center, U.S. Geological Survey (USGS), Gainesville, FL, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States2School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United KingdomSchool of Biological Sciences, The University of Auckland–Waipapa Taumata Rau, Auckland, Aotearoa, New ZealandTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom2School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United KingdomTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States3Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States4Department of Biosciences, University of Milan, Milan, ItalyLOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, Germany5Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United StatesTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom6V.E. Enterprises, Arcada, CA, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United StatesTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United StatesTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom7Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States8Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States9National Institute of Standards and Technology, Charleston, NC, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United StatesTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom0Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Lafayette, LA, United States1Office of Protected Resources, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, MD, United States5Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United StatesLOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, GermanyTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom2New York State College of Veterinary Medicine, Cornell University, Ithaca, NY, United StatesRegenerative Biology, Morgridge Institute for Research, Madison, WI, United States3Zoo Duisburg AG, Duisburg, Germany0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United StatesTree of Life, Wellcome Sanger Institute, Cambridge, United KingdomLOEWE Center for Translational Biodiversity Genomics & Senckenberg Research Institute, Frankfurt, GermanyInstitute of Cell Biology & Neuroscience, Faculty of Biological Sciences, Goethe University, Frankfurt, GermanyTree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom0Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States4Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, United StatesReference 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.https://www.frontiersin.org/articles/10.3389/fmars.2025.1562045/fullreference genomecomparative genomicsconservation genomicswhaledolphinporpoise |
| spellingShingle | 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 Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life Frontiers in Marine Science reference genome comparative genomics conservation genomics whale dolphin porpoise |
| title | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life |
| title_full | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life |
| title_fullStr | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life |
| title_full_unstemmed | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life |
| title_short | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life |
| title_sort | genomic infrastructure for cetacean research and conservation reference genomes for eight families spanning the cetacean tree of life |
| topic | reference genome comparative genomics conservation genomics whale dolphin porpoise |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2025.1562045/full |
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