論文

査読有り
2015年12月

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
  • Jun Inoue
  • ,
  • Yukuto Sato
  • ,
  • Robert Sinclair
  • ,
  • Katsumi Tsukamoto
  • ,
  • Mutsumi Nishida

112
48
開始ページ
14918
終了ページ
14923
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1073/pnas.1507669112
出版者・発行元
NATL ACAD SCIENCES

Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post-teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70-80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.

Web of Science ® 被引用回数 : 90

リンク情報
DOI
https://doi.org/10.1073/pnas.1507669112
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000365988900056&DestApp=WOS_CPL
URL
http://orcid.org/0000-0002-9646-4322
ID情報
  • DOI : 10.1073/pnas.1507669112
  • ISSN : 0027-8424
  • ORCIDのPut Code : 21367534
  • Web of Science ID : WOS:000365988900056

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