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RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839223/ https://www.ncbi.nlm.nih.gov/pubmed/26882984 http://dx.doi.org/10.1093/molbev/msw025 |
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author | Zhong, Xiaoming Peng, Jiguang Shen, Qing Sunny Chen, Jia-Yu Gao, Han Luan, Xuke Yan, Shouyu Huang, Xin Zhang, Shi-Jian Xu, Luying Zhang, Xiuqin Tan, Bertrand Chin-Ming Li, Chuan-Yun |
author_facet | Zhong, Xiaoming Peng, Jiguang Shen, Qing Sunny Chen, Jia-Yu Gao, Han Luan, Xuke Yan, Shouyu Huang, Xin Zhang, Shi-Jian Xu, Luying Zhang, Xiuqin Tan, Bertrand Chin-Ming Li, Chuan-Yun |
author_sort | Zhong, Xiaoming |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4839223 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48392232016-04-22 RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque Zhong, Xiaoming Peng, Jiguang Shen, Qing Sunny Chen, Jia-Yu Gao, Han Luan, Xuke Yan, Shouyu Huang, Xin Zhang, Shi-Jian Xu, Luying Zhang, Xiuqin Tan, Bertrand Chin-Ming Li, Chuan-Yun Mol Biol Evol Resource 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. Oxford University Press 2016-05 2016-02-16 /pmc/articles/PMC4839223/ /pubmed/26882984 http://dx.doi.org/10.1093/molbev/msw025 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Resource Zhong, Xiaoming Peng, Jiguang Shen, Qing Sunny Chen, Jia-Yu Gao, Han Luan, Xuke Yan, Shouyu Huang, Xin Zhang, Shi-Jian Xu, Luying Zhang, Xiuqin Tan, Bertrand Chin-Ming Li, Chuan-Yun RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title | RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title_full | RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title_fullStr | RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title_full_unstemmed | RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title_short | RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque |
title_sort | rhesusbase popgateway: genome-wide population genetics atlas in rhesus macaque |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839223/ https://www.ncbi.nlm.nih.gov/pubmed/26882984 http://dx.doi.org/10.1093/molbev/msw025 |
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