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

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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
Note: Order does not necessarily reflect citation order of authors.
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https://doi.org/10.1186/s13059-016-1071-4Metadata
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Kim, S., Y. S. Cho, H. Kim, O. Chung, H. Kim, S. Jho, H. Seomun, et al. 2016. “Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.” Genome Biology 17 (1): 211. doi:10.1186/s13059-016-1071-4. http://dx.doi.org/10.1186/s13059-016-1071-4.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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1071-4) contains supplementary material, which is available to authorized users.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5090899/pdf/Terms of Use
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