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Genome Biol. 2016 Oct 11;17(1):211.

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

Author information

1
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
2
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
3
Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
4
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
5
Geromics, Ulsan, 44919, Republic of Korea.
6
Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
7
Cheongju Zoo, Cheongju, 28311, Republic of Korea.
8
Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia.
9
Panthera, New York, NY, 10018, USA.
10
Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY, 10460, USA.
11
Department of Ecology, Far Eastern Federal University, Ayaks, Russki Island, Vladivostok, 690950, Russia.
12
Laboratory of Animal Sciences Program, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, 21702, USA.
13
International Zoo Veterinary Group (UK) IZVG LLP, Station House, Parkwood Street, Keighley, BD21 4NQ, UK.
14
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia.
15
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034, Russia.
16
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
17
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
18
Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA.
19
Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
20
Zoological Society of London, London, NW1 4RY, UK.
21
Department of Bioinformatics & Life Science, Soongsil University, Seoul, 06978, Republic of Korea.
22
Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
23
Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
24
Daejeon O-World, Daejeon, 35073, Republic of Korea.
25
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia. lgdchief@gmail.com.
26
Oceanographic Center 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA. lgdchief@gmail.com.
27
The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.
28
Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.
29
Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea. jongbhak@genomics.org.
30
Geromics, Ulsan, 44919, Republic of Korea. jongbhak@genomics.org.
31
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea. y1208@korea.kr.

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; Comparative genomics; De novo assembly; Evolutionary adaptation; Felidae; Leopard

PMID:
27802837
PMCID:
PMC5090899
DOI:
10.1186/s13059-016-1071-4
[Indexed for MEDLINE]
Free PMC Article

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