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

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Authors
Kim, Soonok; Cho, Yun Sung; Kim, Hak-Min; Chung, Oksung; Kim, Hyunho; Jho, Sungwoong; Seomun, Hong; Kim, Jeongho; Bang, Woo Young; Kim, Changmu; An, Junghwa; Bae, Chang Hwan; Bhak, Youngjune; Jeon, Sungwon; Yoon, Hyejun; Kim, Yumi; Jun, JeHoon; Lee, HyeJin; Cho, Suan; Uphyrkina, Olga; Kostyria, Aleksey; Goodrich, John; Miquelle, Dale; Roelke, Melody; Lewis, John; Yurchenko, Andrey; Bankevich, Anton; Cho, Juok; Lee, Semin; Edwards, Jeremy S.; Weber, Jessica A.; Cook, Jo; Kim, Sangsoo; Lee, Hang; Manica, Andrea; Lee, Ilbeum; O’Brien, Stephen J.; Bhak, Jong; Yeo, Joo-Hong
Issue Date
2016-11-02
Publisher
BioMed Central
Citation
Genome Biology, 17(1):211
Keywords
Carnivorous dietEvolutionary adaptationLeopardFelidaeDe novo assemblyComparative genomics
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.
Language
English
URI
https://hdl.handle.net/10371/109880
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College of Veterinary Medicine (수의과대학)Dept. of Veterinary Medicine (수의학과)Journal Papers (저널논문_수의학과)
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