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Mol Biol Evol. 2016 May;33(5):1370-5. doi: 10.1093/molbev/msw025. Epub 2016 Feb 16.

RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque.

Author information

1
Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.
2
Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China Peking-Tsinghua Center for Life Sciences, Beijing, China Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
3
Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan.
4
Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China chuanyunli@pku.edu.cn.

Abstract

Although population genetics studies have significantly accelerated the evolutionary and functional interrogations of genes and regulations, limited polymorphism data are available for rhesus macaque, the model animal closely related to human. Here, we report the first genome-wide effort to identify and visualize the population genetics profile in rhesus macaque. On the basis of the whole-genome sequencing of 31 independent macaque animals, we profiled a comprehensive polymorphism map with 46,146,548 sites. The allele frequency for each polymorphism site, the haplotype structure, as well as multiple population genetics parameters were then calculated on a genome-wide scale. We further developed a specific interface, the RhesusBase PopGateway, to facilitate the visualization of these annotations, and highlighted the applications of this highly integrative platform in clarifying the selection signatures of genes and regulations in the context of the primate evolution. Overall, the updated RhesusBase provides a comprehensive monkey population genetics framework for in-depth evolutionary studies of human biology.

KEYWORDS:

RhesusBase.; population genetics; primate evolution; rhesus macaque; whole-genome sequencing

PMID:
26882984
PMCID:
PMC4839223
DOI:
10.1093/molbev/msw025
[Indexed for MEDLINE]
Free PMC Article

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