1. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly
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Hyunho Kim, Changmu Kim, Chang Hwan Bae, John M. Goodrich, Hong Seomun, John G. Lewis, Suan Cho, Aleksey V. Kostyria, Yun Sung Cho, Sangsoo Kim, Jo Cook, Jessica A. Weber, Andrea Manica, Hyejun Yoon, Jeong-Ho Kim, Sungwoong Jho, Jeremy S. Edwards, Olga Uphyrkina, Hak-Min Kim, Stephen J. O'Brien, Woo Young Bang, Jong Bhak, Sungwon Jeon, JeHoon Jun, Youngjune Bhak, Hang Lee, Semin Lee, Melody E. Roelke, Junghwa An, Ilbeum Lee, Soonok Kim, Hye Jin Lee, Juok Cho, Oksung Chung, Joo-Hong Yeo, Anton Bankevich, Andrey A. Yurchenko, Dale G. Miquelle, Yumi Kim, Manica, Andrea [0000-0003-1895-450X], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Felidae ,Population ,Zoology ,Evolutionary adaptation ,03 medical and health sciences ,0302 clinical medicine ,biology.animal ,De novo assembly ,Animals ,Panthera ,Herbivory ,Carnivore ,education ,Phylogeny ,Comparative genomics ,Carnivorous diet ,Mammals ,education.field_of_study ,Genome ,biology ,Research ,Leopard ,Genetic Variation ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,biology.organism_classification ,Adaptation, Physiological ,Biological Evolution ,Amur leopard ,030104 developmental biology ,Evolutionary biology ,Cats ,Omnivore ,Adaptation ,030217 neurology & neurosurgery - 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.
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