Resolving ray-finned fish phylogeny with genomic data: Developing an analysis pipeline for identification of homologous genes

• Project/Area Number: 24770070
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biodiversity/Systematics
• Research Institution: Okinawa Institute of Science and Technology Graduate University (2013-2015); The University of Tokyo (2012)
• Principal Investigator: Inoue Jun 沖縄科学技術大学院大学, Mathematical Biology, スタッフサイエンティスト (10596779)
• Research Collaborator: NISHIDA Mutsumi 琉球大学, 理事 (90136896) ; TSUKAMOTO Katsumi 日本大学, 海洋生物資源科学科, 教授 (10090474) ; SINCLAIR Robert 沖縄科学技術大学院大学, Mathematical Biology, 准教授 (50423744) ; SATO Yukuto 東北大学, 東北メディカルメガバンク機構, 助教 (20566418)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 全ゲノム重複 / 真骨魚類 / 分子系統 / 真骨類

Outline of Final Research Achievements

This study constructed an analysis pipeline to identify marker genes from genomic data for phylogenetic studies of ray-finned fishes. The pipeline was developed by implementing cutting-edge methods of molecular phylogenetics and by analyzing all protein-coding gene sequences of 15 vertebrates. Genome structural comparisons among vertebrates suggest that common structure of teleost genomes were established just after whole genome duplication occurred in the ancestor of all extant teleosts.

Research Products

• [Journal Article] Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling (2015)
  • Author(s): Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, T., and Nishida, M.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 112 Issue: 48 Pages: 14918-14923
  • DOI: 10.1073/pnas.1507669112
  • Peer Reviewed / Open Access
• [Presentation] Identification of phylogenetic marker gene considering whole genome duplication and species tree (2015)
  • Author(s): Inoue J., Sato, Y., Sinclair, R., Nishida, M.
  • Organizer: Introduction to the analysis of molecular evolution in the genomic era.
  • Place of Presentation: Fudan University, Shanghai
  • Year and Date: 2015-11-06
  • Int'l Joint Research / Invited
• [Presentation] 全ゲノム重複と種の系統樹を考慮した系統解析マーカ遺伝子の選定 (2015)
  • Author(s): 井上 潤，佐藤 行人，シンクレア ロバート，塚本 勝巳，西田 睦
  • Organizer: 日本進化学会年会
  • Place of Presentation: 中央大学，東京
  • Year and Date: 2015-08-20
  • Invited
• [Presentation] Selecting molecular markers from transcriptome data for fish phylogenetics. (2014)
  • Author(s): Inoue J., Sato, Y., Sinclair, R., Nishida, M.
  • Organizer: Workshop on Methods for Biodiversity Research,
  • Place of Presentation: Fudan Univ., Shanghai
• [Presentation] 脊椎動物 3 億年のゲノム進化：ゲノム重複に由来する遺伝子の保持と進化に寄与した自然選択項の検出． (2013)
  • Author(s): 井上 潤，佐藤 行人，西田 睦．
  • Organizer: 日本進化学会
  • Place of Presentation: 筑波大学
• [Presentation] 真骨魚類ゲノムの進化特性: トランスクリプトーム相同遺伝子データベースの構築． (2012)
  • Author(s): 井上 潤
  • Organizer: 日本進化学会年会
  • Place of Presentation: 首都大学東京
• [Remarks] FishOrthoDB
  • URL: http://fish-evol.unit.oist.jp/cgi-bin/TGD.cgi