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Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

ABSTRACT: With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, RhesusBase2 refined the fine-scale structures in 30% of the macaque Ensembl transcripts, reporting an accurate, up-to-date set of macaque gene models. On the basis of these annotations and accurate macaque gene models, we further developed an NGS-oriented Molecular Evolution Gateway to access and visualize macaque annotations in reference to human orthologous genes and associated regulations (www.rhesusbase.org/molEvo). We highlighted the application of this well-annotated genomic framework in generating hypothetical link of human-biased regulations to human-specific traits, by using mechanistic characterization of the DIEXF gene as an example that provides novel clues to the understanding of digestive system reduction in human evolution. On a global scale, we also identified a catalog of 9,295 human-biased regulatory events, which may represent novel elements that have a substantial impact on shaping human transcriptome and possibly underpin recent human phenotypic evolution. Taken together, we provide an NGS data-driven, information-rich framework that will broadly benefit genomics research in general and serves as an important resource for in-depth evolutionary studies of human biology.

SUBMITTER: Zhang SJ

PROVIDER: S-EPMC3995340 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

Zhang Shi-Jian SJ Liu Chu-Jun CJ Yu Peng P Zhong Xiaoming X Chen Jia-Yu JY Yang Xinzhuang X Peng Jiguang J Yan Shouyu S Wang Chenqu C Zhu Xiaotong X Xiong Jingwei J Zhang Yong E YE Tan Bertrand Chin-Ming BC Li Chuan-Yun CY

Molecular biology and evolution 20140227 5

With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS ...[more]

PMID: 24577841

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Dataset Information

Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

Publications

Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

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