Comprehensive analysis of genome duplication on genome evolution

• Project/Area Number: 16H06154
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: System genome science
• Research Institution: The University of Tokyo
• Principal Investigator: Iwasaki Wataru 東京大学, 大学院理学系研究科(理学部), 准教授 (50545019)
• Project Period (FY): 2016-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥26,650,000 (Direct Cost: ¥20,500,000、Indirect Cost: ¥6,150,000); Fiscal Year 2019: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000); Fiscal Year 2018: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000); Fiscal Year 2017: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000); Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: ゲノム / 進化 / バイオインフォマティクス / ゲノム進化

Outline of Final Research Achievements

In this study, quality of Trichosporon genome data was first improved. Subsequently, they were fed into integrative analysis with transcriptome data. Specifically, we showed that early post-hybridization evolutionary processes occur separately at the gene sequence and gene expression levels but together contribute to the stabilization of hybrid genome and transcriptome.

Academic Significance and Societal Importance of the Research Achievements

現在の生物が持つ多様な性質は、長い進化の結果獲得されたものである。異なるゲノムが合わさって新たな生物種を生み出す「ハイブリッド化」は、そうした新しい性質を持つ生物種の進化に繋がる重要なイベントだと考えられているが、どうしてそういった現象が可能になるのか、重要な部分が謎として残っていた。本研究では、そうした進化がどうして可能となるのか、そのメカニズムを解明した。

Research Products

• [Int'l Joint Research] チュラロンコーン大学(タイ)
• [Int'l Joint Research] チュラーロンコーン大学(タイ)
• [Int'l Joint Research] チュラーロンコーン大学(タイ)
• [Journal Article] Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction (2019)
  • Author(s): Matsui Motomu、Iwasaki Wataru
  • Journal Title: Systematic Biology Volume: 69 Pages: 265-279
  • DOI: 10.1093/sysbio/syz049
  • Peer Reviewed / Open Access
• [Journal Article] Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi (2019)
  • Author(s): Sriswasdi Sira、Takashima Masako、Manabe Ri-ichiroh、Ohkuma Moriya、Iwasaki Wataru
  • Journal Title: Communications Biology Volume: 2 Issue: 1 Pages: 263-263
  • DOI: 10.1038/s42003-019-0515-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios (2019)
  • Author(s): Ishikawa Sohta A、Zhukova Anna、Iwasaki Wataru、Gascuel Olivier
  • Journal Title: Molecular Biology and Evolution Volume: 36 Issue: 9 Pages: 2069-2085
  • DOI: 10.1093/molbev/msz131
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community (2019)
  • Author(s): Hiraoka Satoshi、Okazaki Yusuke、Anda Mizue、Toyoda Atsushi、Nakano Shin-ichi、Iwasaki Wataru
  • Journal Title: Nature Communications Volume: 10 Issue: 1 Pages: 159-159
  • DOI: 10.1038/s41467-018-08103-y
  • NAID: 120006879468
  • Peer Reviewed / Open Access
• [Journal Article] SonicParanoid: fast, accurate and easy orthology inference (2018)
  • Author(s): Cosentino Salvatore、Iwasaki Wataru
  • Journal Title: Bioinformatics Volume: 35 Issue: 1 Pages: 149-151
  • DOI: 10.1093/bioinformatics/bty631
  • Peer Reviewed / Open Access
• [Journal Article] Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia (2018)
  • Author(s): Kumagai Yohei、Yoshizawa Susumu、Nakajima Yu、Watanabe Mai、Fukunaga Tsukasa、Ogura Yoshitoshi、Hayashi Tetsuya、Oshima Kenshiro、Hattori Masahira、Ikeuchi Masahiko、Kogure Kazuhiro、DeLong Edward F.、Iwasaki Wataru
  • Journal Title: The ISME Journal Volume: in press Issue: 5 Pages: 1329-1343
  • DOI: 10.1038/s41396-018-0058-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved ‘natural’ hybrid genomes (2017)
  • Author(s): Takashima Masako、Sriswasdi Sira、Manabe Ri-Ichiroh、Ohkuma Moriya、Sugita Takashi、Iwasaki Wataru
  • Journal Title: Yeast Volume: 35 Issue: 1 Pages: 99-111
  • DOI: 10.1002/yea.3284
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan (2017)
  • Author(s): Hiraoka Satoshi、Miyahara Masaya、Fujii Kazushi、Machiyama Asako、Iwasaki Wataru
  • Journal Title: Frontiers in Microbiology Volume: 8 Pages: 1506-1506
  • DOI: 10.3389/fmicb.2017.01506
  • Peer Reviewed / Open Access
• [Journal Article] Phylogeography of the yellowfin goby Acanthogobius flavimanus in native and non-native distributions. (2017)
  • Author(s): Shotaro Hirase, Sherrie Chambers, Kathryn Hassell, Melissa Carew, Vincent Pettigrove, Kiyoshi Soyano, Masaki Nagae, and Wataru Iwasaki.
  • Journal Title: Marine Biology Volume: 164 Issue: 5 Pages: 106-106
  • DOI: 10.1007/s00227-017-3137-6
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants (2017)
  • Author(s): Tsukasa Fukunaga and Wataru Iwasaki
  • Journal Title: BMC Bioinformatics Volume: 18 Issue: 1 Pages: 46-46
  • DOI: 10.1186/s12859-016-1408-8
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Global deceleration of gene evolution following recent genome hybridizations in fungi. (2016)
  • Author(s): Sira Sriswasdi, Masako Takashima, Ri-ichiroh Manabe, Moriya Ohkuma, Takashi Sugita, and Wataru Iwasaki.
  • Journal Title: Genome Research Volume: 26 Issue: 8 Pages: 1081-1090
  • DOI: 10.1101/gr.205948.116
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] 比較ゲノム解析・微生物群集解析・表現型データ解析のバイオインフォマティクス (2019)
  • Author(s): 岩崎渉
  • Organizer: 第92回日本生化学会大会
  • Invited
• [Presentation] 生物進化・生態のバイオインフォマティクス (2019)
  • Author(s): 岩崎渉
  • Organizer: 第42回日本分子生物学会年会
  • Invited
• [Presentation] データ駆動アプローチによるゲノム微生物学の拡張 (2019)
  • Author(s): 岩崎渉
  • Organizer: 第13回日本ゲノム微生物学会年会
  • Invited
• [Presentation] 大規模ゲノム進化研究のためのデータベース・ソフトウェア (2018)
  • Author(s): 岩崎渉
  • Organizer: 日本進化学会第20回大会
  • Invited
• [Presentation] トリコスポロン属酵母ハイブリッドゲノムにおける遺伝子進化速度の低下 (2017)
  • Author(s): 岩崎渉，Sriswasdi Sira，高島昌子，眞鍋理一郎，大熊盛也，杉田隆
  • Organizer: 第11回日本ゲノム微生物学会年会
  • Place of Presentation: 慶應義塾大学湘南藤沢キャンパス（神奈川県藤沢市）
  • Year and Date: 2017-03-02
• [Presentation] How do microbes spread across environmental barriers? (2017)
  • Author(s): Wataru Iwasaki
  • Organizer: The 9th Asian Symposium on Microbial Ecology
  • Int'l Joint Research / Invited
• [Presentation] データベース・カルチャーコレクションでひもとく微生物の進化 (2017)
  • Author(s): 岩崎渉
  • Organizer: 環境微生物系学会合同大会2017
  • Invited
• [Presentation] 分子系統学とバイオインフォマティクス (2017)
  • Author(s): 岩崎渉
  • Organizer: 第207回農林交流センターワークショップ
  • Invited
• [Presentation] バイオインフォマティクスでひもとく生命進化の道のり (2016)
  • Author(s): 岩崎渉
  • Organizer: 早稲田大学先進理工学部電気・情報生命工学科講演会
  • Place of Presentation: 早稲田大学西早稲田キャンパス（東京都新宿区）
  • Invited
• [Remarks] 研究者個人ウェブページ
  • URL: http://iwasakilab.bs.s.u-tokyo.ac.jp/iwasaki/publications.html