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 a...

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Published in:	Genome Biology Vol. 17; no. 1; p. 211
Main 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
Format:	Journal Article
Language:	English
Published:	England BioMed Central 11-10-2016
Subjects:	Acinonyx jubatus Adaptation, Physiological - genetics Adaptations Animals Bioinformatics Biological Evolution Bovidae Carnivores Cats Conservation status Diet Evolution Felidae Felis catus Gene families Genes Genetic diversity Genetic Variation Genome Genomes Genomic analysis Herbivores Herbivory - genetics Hominidae Hunting Mammals - genetics Meat Mitochondrial DNA Molecular Sequence Annotation Muscle strength Panthera - genetics Panthera leo Panthera pardus Panthera tigris Phylogeny Physiology Prionailurus bengalensis Proteins Sequence Analysis, DNA Specialization Wildcats Comparative genomics Leopard Felidae Carnivorous diet De novo assembly Evolutionary adaptation
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-016-1071-4