Soonok Kim^1†, Yun Sung Cho^2,3,4†, Hak-Min Kim^2,3†, Oksung Chung⁴, Hyunho Kim⁵, Sungwoong Jho⁴, Hong Seomun⁶, Jeongho Kim⁷, Woo Young Bang¹, Changmu Kim¹, Junghwa An⁶, Chang Hwan Bae¹, Youngjune Bhak², Sungwon Jeon^2,3, Hyejun Yoon^2,3, Yumi Kim², JeHoon Jun^4,5, HyeJin Lee^4,5, Suan Cho^4,5, Olga Uphyrkina⁸, Aleksey Kostyria⁸, John Goodrich⁹, Dale Miquelle^10,11, Melody Roelke¹², John Lewis¹³, Andrey Yurchenko¹⁴, Anton Bankevich¹⁵, Juok Cho¹⁶, Semin Lee^2,3,17, Jeremy S. Edwards¹⁸, Jessica A. Weber¹⁹, Jo Cook²⁰, Sangsoo Kim²¹, Hang Lee²², Andrea Manica²³, Ilbeum Lee²⁴, Stephen J. O’Brien^14,25*, Jong Bhak^2,3,4,5* and Joo-Hong Yeo<sup>1*

1</sup>Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea. ²The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea. ³Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea. ⁴Personal Genomics Institute, Genome Research Foundation, Cheongju 28160, Republic of Korea. ⁵Geromics, Ulsan 44919, Republic of Korea. ⁶Animal Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea. ⁷Cheongju Zoo, Cheongju 28311, Republic of Korea. ⁸Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia. ⁹Panthera, New York, NY 10018, USA. ¹⁰Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY 10460, USA. ¹¹Department of Ecology, Far Eastern Federal University, Ayaks, Russki Island, Vladivostok 690950, Russia. ¹²Laboratory of Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702, USA. ¹³International Zoo Veterinary Group (UK) IZVG LLP, Station House, Parkwood Street, Keighley BD21 4NQ, UK. ¹⁴Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia. ¹⁵Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia. ¹⁶Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. ¹⁷Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA. ¹⁸Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA. ¹⁹Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA. ²⁰Zoological Society of London, London NW1 4RY, UK. ²¹Department of Bioinformatics & Life Science, Soongsil University, Seoul 06978, Republic of Korea. ²²Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea. ²³Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. ²⁴Daejeon O-World, Daejeon 35073, Republic of Korea. ²⁵Oceanographic Center 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL 33004, USA.

^†Equal contributors

^* Correspondence : Stephen J. O’Brien, Jong Bhak, Joo-Hong Yeo

Abstract

Background
There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.

Results
We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.

Conclusions
Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

Keywords : Carnivorous diet, Evolutionary adaptation, Leopard, Felidae, De novo assembly, Comparative genomics