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

Phillip A Morin^1*Bernhard Bein^2,3Chiara Bortoluzzi⁴Yury V Bukhman⁵Taylor Hains^6,7Dorothea Heimeier^8,9Marcela Uliano-Silva¹⁰Dominic E Absolon¹⁰Linelle Abueg¹¹Jessica Antosiewicz- Bourget⁵Jennifer R Balacco¹¹Robert Bonde¹²Nadolina Brajuka¹¹Andrew C Brownlow¹³Emma L Carroll⁸Molly Carter¹⁴Joanna Collins¹⁰Nicholas John Davison¹³Amy Denton¹⁰Olivier Fedrigo¹¹Giulio Formenti¹¹Andrew Foote¹⁵Guido Gallo¹⁶Carola Greve²Marlys L Houck¹⁷Caroline Howard¹⁰Jeff Jacobsen¹⁸Nivesh Jain¹¹Ksenia Krasheninnikova¹⁰Brigid Mary Maloney¹¹Bethan F Manley¹⁰Thomas C Mathers¹⁰Shane A Mccarthy¹⁰Michael R Mcgowen¹⁹Susanne Meyer²⁰Jacquelyn Mountcastle, MPH¹¹Benjamin Adam Neely²¹Brian O'toole¹¹Sarah Pelan¹⁰P Rosel²²Teri K Rowles²³Oliver A Ryder¹⁷Tilman Schell²Ying Sims¹⁰Judy St Leger²⁴Ron Stewart⁵Kerstin Ternes²⁵Tatiana Tilley¹¹Conor Whelan¹¹Jonathan Wood¹⁰Michael Hiller^26*Mark Blaxter^27*Erich David Jarvis^28,29*

• ¹Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, La Jolla, United States
• ²LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany, Frankfurt, Germany
• ³Institute of Cell Biology & Neuroscience, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
• ⁴Wellcome Sanger Institute (WT), Hinxton, Cambridgeshire, United Kingdom
• ⁵Morgridge Institute for Research, Madison, Wisconsin, United States
• ⁶Committee on Evolutionary Biology, The University of Chicago, Chicago, Illinois, United States
• ⁷Earth Sciences, Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, United States
• ⁸School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, Auckland, New Zealand
• ⁹Faculty of Life Sciences and Aquaculture, Nord University, Bodø, Nordland, Norway
• ¹⁰Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
• ¹¹Vertebrate Genome Laboratory, The Rockefeller University, New York, United States
• ¹²Wetland and Aquatic Research Center, United States Geological Survey (USGS), Gainesville, FL, United States
• ¹³School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
• ¹⁴Wellcome Genome Campus, Hinxton, United Kingdom
• ¹⁵Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
• ¹⁶Department of Biosciences, University of Milan, Milan, Lombardy, Italy
• ¹⁷Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
• ¹⁸V.E. Enterprises, Arcata, CA, United States
• ¹⁹Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
• ²⁰Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States
• ²¹Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, South Carolina, United States
• ²²Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, LA, United States
• ²³Office of Protected Resources, NOAA Fisheries, Silver Spring, Maryland, United States
• ²⁴New York State College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
• ²⁵Zoo Duisburg AG, Duisburg, North Rhine-Westphalia, Germany
• ²⁶Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse, Germany
• ²⁷Tree of Life, Wellcome Sanger Institute (WT), Hinxton, Cambridgeshire, United Kingdom
• ²⁸Vertebrate Genome Laboratory, The Rockefeller University, New York City, New York, United States
• ²⁹Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland, United States

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.