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Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys

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Title: Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys
Authors: Ikeda, Masaki Browse this author
Satomura, Kazuhiro Browse this author
Sekizuka, Tsuyoshi Browse this author →KAKEN DB
Hanada, Kentaro Browse this author →KAKEN DB
Endo, Toshinori Browse this author →KAKEN DB
Osada, Naoki Browse this author →KAKEN DB
Keywords: Evolution
Old World monkey
Issue Date: Jul-2018
Publisher: John Wiley & Sons
Journal Title: American journal of primatology
Volume: 80
Issue: 7
Start Page: e22882
Publisher DOI: 10.1002/ajp.22882
PMID: 29896810
Abstract: Simian retrovirus (SRV) is a type-D betaretrovirus infectious to the Old World monkeys causing a variety of symptoms. SRVs are also present in the Old World monkey genomes as endogenous forms, which are referred to as Simian endogenous retroviruses (SERVs). Although many SERV sequences have been identified in Cercopithecinae genomes, with potential of encoding all functional genes, the distribution of SERVs in genomes and evolutionary relationship between exogeneous SRVs and SERVs remains unclear. In this study, we comprehensively investigated seven draft genome sequences of the Old World monkeys, and identified a novel cluster of SERVs in the two Rhinopithecus (R. roxellana and R. bieti) genomes, which belong to the Colobinae subfamily. The Rhinopithecus genomes harbored higher copy numbers of SERVs than the Cercopithecinae genomes. A reconstructed phylogenetic tree showed that the Colobinae SERVs formed a distinct cluster from SRVs and Cercopithecinae SERVs, and more closely related to exogenous SRVs than Cercopithecinae SERVs. Three radical amino acid substitutions specific to Cercopithecinae SERVs, which potentially affect the infectious ability of SERVs, were also identified in the proviral envelope protein. In addition, we found many integration events of SERVs were genus- or species-specific, suggesting the recent activity of SERVs in the Old World monkey genomes. The results suggest that SERVs in Cercopithecinae and Colobinae monkeys were endogenized after the divergence of subfamilies and do not transmit across subfamilies. Our findings also support the hypothesis that Colobinae SERVs are direct ancestors of SRV-6, which has a different origin from the other exogenous SRVs. These findings shed novel insight into the evolutionary history of SERVs, and may help to understand the process of endogenization of SRVs.
Rights: This is the peer reviewed version of the following article: Ikeda M, Satomura K, Sekizuka T,Hanada K, Endo T, Osada N. Comprehensive phylogenomicanalysis reveals a novel cluster of simian endogenousretroviral sequences in Colobinae monkeys.Am J Primatol.2018;80:e22882., which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.
Type: article (author version)
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
国際連携研究教育局 : GI-CoRE (Global Institution for Collaborative Research and Education : GI-CoRE) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 長田 直樹

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