Determining phylogenetic positions of species with accelerated evolutionary rates by genome-wide analyses: a case study on urochordate Larvaceans

• Project/Area Number: 18K06396
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 45030:Biodiversity and systematics-related
• Research Institution: The University of Tokyo (2020-2022); National Institute of Genetics (2019); Okinawa Institute of Science and Technology Graduate University (2018)
• Principal Investigator: Inoue Jun 東京大学, 大気海洋研究所, 准教授 (10596779)
• Co-Investigator(Kenkyū-buntansha): 西野 敦雄 弘前大学, 農学生命科学部, 教授 (50343116)
• Project Period (FY): 2018-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2020: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: ゲノム比較 / 解析パイプライン / オタマボヤ類 / 全タンパク質遺伝子解析パイプライン / トランスクリプトームデータ / 遊泳性尾索動物 / トランスクリプトームデータ。 / 全タンパク質遺伝子解析パイプライン。 / 分子系統解析 / 全タンパク質遺伝子解読 / オタマボヤ / ゲノム系統解析 / 尾索類 / 遺伝子系統樹 / トランスクリプトーム / 脊索動物

Outline of Final Research Achievements

In order to determine phylogenetic positions of species with accelerated substitution rates of gene sequences, I developed ORTHOSCOPE* (star). ORTHOSCOPE* estimates phylogenetic trees for all protein-coding gene sequences. By using supercomputers, users can estimate phylogenetic positions of focal species by employing gene models available from web version (https://github.com/jun-inoue/orthoscope). Moreover, users can estimate phylogenetic positions of whole genome duplications and evaluate presence or absence of horizontal gene transfer events.

Academic Significance and Societal Importance of the Research Achievements

学術的意義：分子系統解析を専門としない研究者であっても，遺伝子系統樹に基づいてゲノムの進化を考察できるようになった点。
社会的意義：いまだに「解析スピードが速いため巨大なデータを解析できる」だけで正確さを追求しない解析ツールが出回る本研究分野に、50 年以上の歴史をもつ分子系統解析を取り入れた解析ツールを提供することで、軌道修正のチャンスを提供した点。

Research Products

• [Journal Article] Active Expression of Genes for Protein Modification Enzymes in Habu Venom Glands (2022)
  • Author(s): Akiko Isomoto、Eiichi Shoguchi、Kanako Hisata、Jun Inoue、Yinrui Sun、Kenji Inaba、Noriyuki Satoh、Tomohisa Ogawa、Hiroki Shibata
  • Journal Title: Toxins Volume: 14 Issue: 5 Pages: 300-300
  • DOI: 10.3390/toxins14050300
  • Peer Reviewed / Open Access
• [Journal Article] Two Hidden mtDNA-Clades of Crown-of-Thorns Starfish in the Pacific Ocean (2022)
  • Author(s): Yasuda Nina、Inoue Jun、Hall Michael R.、Nair Manoj R.、Adjeroud Mehdi、Fortes Miguel D.、Nishida Mutsumi、Tuivavalagi Nat、Ravago-Gotanco Rachel、Forsman Zac H.、Soliman Taha、Koyanagi Ryo、Hisata Kanako、Motti Cherie A.、Satoh Noriyuki
  • Journal Title: Frontiers in Marine Science Volume: 9 Pages: 831240-831240
  • DOI: 10.3389/fmars.2022.831240
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data (2021)
  • Author(s): Inoue Jun
  • Journal Title: Molecular Biology and Evolution Volume: 39 Issue: 1 Pages: 1-10
  • DOI: 10.1093/molbev/msab301
  • Peer Reviewed / Open Access
• [Journal Article] Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding (2021)
  • Author(s): Shinzato Chuya、Narisoko Haruhi、Nishitsuji Koki、Nagata Tomofumi、Satoh Noriyuki、Inoue Jun
  • Journal Title: Frontiers in Marine Science Volume: 8 Pages: 1-9
  • DOI: 10.3389/fmars.2021.758207
  • Peer Reviewed / Open Access
• [Journal Article] A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum (2021)
  • Author(s): Satoh Noriyuki、Tominaga Hitoshi、Kiyomoto Masato、Hisata Kanako、Inoue Jun、Nishitsuji Koki
  • Journal Title: Frontiers in Cell and Developmental Biology Volume: 9 Pages: 1-16
  • DOI: 10.3389/fcell.2021.696875
• [Journal Article] Commentary on ORTHOSCOPE: a web tool for genome comparisons. (2021)
  • Author(s): Inoue, J.
  • Journal Title: Journal of Genetics and Genomes Volume: 5 Pages: 1-1
  • Peer Reviewed / Open Access
• [Journal Article] dbCNS: A New Database for Conserved Noncoding Sequences (2020)
  • Author(s): Inoue Jun、Saitou Naruya
  • Journal Title: Molecular Biology and Evolution Volume: 38 Issue: 4 Pages: 1665-1676
  • DOI: 10.1093/molbev/msaa296
  • Peer Reviewed / Open Access
• [Journal Article] Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes (2020)
  • Author(s): Shinzato Chuya、Khalturin Konstantin、Inoue Jun、Zayasu Yuna、Kanda Miyuki、Kawamitsu Mayumi、Yoshioka Yuki、Yamashita Hiroshi、Suzuki Go、Satoh Noriyuki
  • Journal Title: Molecular Biology and Evolution Volume: 38 Issue: 1 Pages: 16-30
  • DOI: 10.1093/molbev/msaa216
  • Peer Reviewed / Open Access
• [Journal Article] Identification of ancient viruses from metagenomic data of the Jomon people (2020)
  • Author(s): Nishimura Luca、Sugimoto Ryota、Inoue Jun、Nakaoka Hirofumi、Kanzawa-Kiriyama Hideaki、Shinoda Ken-ichi、Inoue Ituro
  • Journal Title: Journal of Human Genetics Volume: 66 Issue: 3 Pages: 287-296
  • DOI: 10.1038/s10038-020-00841-6
  • Peer Reviewed / Open Access
• [Journal Article] Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer (2020)
  • Author(s): Kun-Lung Li, Keisuke Nakashima, Jun Inoue, and Noriyuki Satoh
  • Journal Title: Genes Volume: 11 Issue: 8 Pages: 937-937
  • DOI: 10.3390/genes11080937
  • Peer Reviewed / Open Access
• [Journal Article] An Investigation into the Genetic History of Japanese Populations of Three Starfish, Acanthaster planci, Linckia laevigata, and Asterias amurensis, Based on Complete Mitochondrial DNA Sequences (2020)
  • Author(s): Inoue Jun、Hisata Kanako、Yasuda Nina、Satoh Noriyuki
  • Journal Title: G3: Genes|Genomes|Genetics Volume: 10 Issue: 7 Pages: 2519-2528
  • DOI: 10.1534/g3.120.401155
  • Peer Reviewed / Open Access
• [Journal Article] ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes (2019)
  • Author(s): Jun Inoue, Keisuke Nakashima, and Noriyuki Satoh
  • Journal Title: Genes Volume: 10 Issue: 4 Pages: 1-9
  • DOI: 10.3390/genes10040294
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa (2018)
  • Author(s): Inoue Jun、Satoh Noriyuki
  • Journal Title: Molecular Biology and Evolution Volume: 36 Issue: 3 Pages: 621-631
  • DOI: 10.1093/molbev/msy226
  • Peer Reviewed / Open Access
• [Presentation] ORTHOSCOPE* ：ゲノムに存在する全遺伝子の歴史を推定する系統解析パイプライン (2022)
  • Author(s): 井上 潤
  • Organizer: 日本動物学会
• [Presentation] 系統樹に基づいたゲノム比較 (2022)
  • Author(s): 井上 潤
  • Organizer: 生命科学を支える分子系統学
  • Invited
• [Presentation] dbCNS: 進化的に保存された非コード配列の新たなデータベース (2021)
  • Author(s): 井上 潤、斎藤成也
  • Organizer: 日本動物学会オンライン米子大会
• [Presentation] Using dbCNS, a database of conserved noncoding sequences (2021)
  • Author(s): 井上 潤
  • Organizer: 遺伝研共同研究会「日本列島人の起源と成立をゲノム情報から探る」
  • Invited
• [Presentation] dbCNS: a new database for conserved non-coding sequencess (2021)
  • Author(s): Inoue, J.
  • Organizer: Genome Concept Centennial Symposium
  • Int'l Joint Research / Invited
• [Presentation] 脊椎動物の頭部筋肉に特異的なミオシン重鎖遺伝子MYH16 の起源と進化 (2020)
  • Author(s): 西野純子、井上 潤、神田真司、西野敦雄
  • Organizer: 日本動物学会・東北支部大会
• [Presentation] 縄文人由来 DNA を用いた古代微生物の配列解析 (2020)
  • Author(s): 西村瑠佳、杉本竜太、井上 潤、中岡博史、神澤秀明、篠田謙一、井ノ上逸郎
  • Organizer: 日本進化学会
• [Presentation] 種の系統樹に基づいて左右相称動物のオーソログを判定するウェブツールの開発． (2018)
  • Author(s): 井上 潤，佐藤 矩行．
  • Organizer: 日本動物学会 第89 回大会 (代替)
• [Book] ヒトゲノム事典 (2021)
  • Author(s): 井ノ上 逸朗, 今西 規, 河村 正二, 斎藤 成也, 颯田 葉子, 田嶋 敦
  • Total Pages: 448
  • Publisher: 一色出版
  • ISBN: 9784910389127
• [Remarks] ORTHOSCOPE*
  • URL: https://github.com/jun-inoue/ORTHOSCOPE_STAR
• [Remarks] ORTHOSCOPE
  • URL: https://github.com/jun-inoue/orthoscope
• [Remarks] dbCNS
  • URL: https://github.com/jun-inoue/dbCNS