Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.
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.



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.



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.
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Soonok
S
Kim
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
Yun Sung
YS
Cho
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Hak-Min
HM
Kim
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
Oksung
O
Chung
Geromics, Ulsan, 44919, Republic of Korea.
Hyunho
H
Kim
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
Sungwoong
S
Jho
Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Hong
H
Seomun
Cheongju Zoo, Cheongju, 28311, Republic of Korea.
Jeongho
J
Kim
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Woo Young
WY
Bang
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Changmu
C
Kim
Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Junghwa
J
An
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Chang Hwan
CH
Bae
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Youngjune
Y
Bhak
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Sungwon
S
Jeon
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Hyejun
H
Yoon
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Yumi
Y
Kim
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.|Geromics, Ulsan, 44919, Republic of Korea.
JeHoon
J
Jun
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.|Geromics, Ulsan, 44919, Republic of Korea.
HyeJin
H
Lee
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.|Geromics, Ulsan, 44919, Republic of Korea.
Suan
S
Cho
Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia.
Olga
O
Uphyrkina
Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia.
Aleksey
A
Kostyria
Panthera, New York, NY, 10018, USA.
John
J
Goodrich
Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY, 10460, USA.|Department of Ecology, Far Eastern Federal University, Ayaks, Russki Island, Vladivostok, 690950, Russia.
Dale
D
Miquelle
Laboratory of Animal Sciences Program, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, 21702, USA.
Melody
M
Roelke
International Zoo Veterinary Group (UK) IZVG LLP, Station House, Parkwood Street, Keighley, BD21 4NQ, UK.
John
J
Lewis
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia.
Andrey
A
Yurchenko
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034, Russia.
Anton
A
Bankevich
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Juok
J
Cho
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.|Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
Semin
S
Lee
Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA.
Jeremy S
JS
Edwards
Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
Jessica A
JA
Weber
Zoological Society of London, London, NW1 4RY, UK.
Jo
J
Cook
Department of Bioinformatics & Life Science, Soongsil University, Seoul, 06978, Republic of Korea.
Sangsoo
S
Kim
Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
Hang
H
Lee
Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
Andrea
A
Manica
Daejeon O-World, Daejeon, 35073, Republic of Korea.
Ilbeum
I
Lee
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia. lgdchief@gmail.com.|Oceanographic Center 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA. lgdchief@gmail.com.
Stephen J
SJ
O'Brien
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.|Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea. jongbhak@genomics.org.|Geromics, Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.
Jong
J
Bhak
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea. y1208@korea.kr.
Joo-Hong
JH
Yeo
D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D005075:Biological Evolution; D002415:Cats; D014644:Genetic Variation; D016678:Genome; D060434:Herbivory / Q000235:genetics; D008322:Mammals / Q000235:genetics; D058977:Molecular Sequence Annotation; D046009:Panthera / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
Carnivorous diet; Comparative genomics; De novo assembly; Evolutionary adaptation; Felidae; Leopard