A holistic ecosystemic investigation of marine giruses, virophages and their eukaryotic hosts

• Project/Area Number: 26430184
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Genome biology
• Research Institution: Kyoto University
• Principal Investigator: Ogata Hiroyuki 京都大学, 化学研究所, 教授 (70291432)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 巨大ウイルス / 海洋ウイルス / 海洋生態系 / メタゲノム / 多様性 / 微生物生態 / 海洋微生物 / Tara Oceans / ウイルス－宿主相互作用 / 海洋メタゲノム / 微生物多様性 / タラ海洋探査（②フランス）

Outline of Final Research Achievements

Based on a global scale eukaryotic metatranscriptomic data, we revealed that giant viruses actively infect their hosts everywhere at every depth examined. Newly designed PCR primers were used to reveal the existence of over 6,000 genotypes for giant viruses (Megaviridae) in a single water sample collected at Osaka Bay. Developed bioinformatics tools are made publicly accessible through internet (http://www.genome.jp/viptree/, http://www.genome.jp/virushostdb/).

Research Products

• [Int'l Joint Research] CNRS(フランス)
• [Int'l Joint Research] Ohaio State University(米国)
• [Int'l Joint Research] Aix-Marseille University(フランス)
• [Int'l Joint Research] EMBL(ドイツ)
• [Int'l Joint Research] Genoscope(フランス)
• [Int'l Joint Research] ＣＮＲＳ(フランス)
• [Int'l Joint Research] ＥＭＢＬ(ドイツ)
• [Int'l Joint Research] アリゾナ大学(米国)
• [Journal Article] ViPTree: the viral proteomic tree server (2017)
  • Author(s): Nishimura Y., Yoshida T., Kuronishi M., Uehara H., Ogata H., Goto S.
  • Journal Title: Bioinformatics Volume: 印刷中 Issue: 15 Pages: 1-2
  • DOI: 10.1093/bioinformatics/btx157
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Environmental viral genomes shed new light on virus-host interactions in the ocean (2017)
  • Author(s): Nishimura Y., Watai H., Honda T., Mihara T., Omae K., Roux S., Blanc-Mathieu R., Yamamoto K., Hingamp P., Sako Y., Sullivan M.B., Goto S., Ogata H., Yoshida T.
  • Journal Title: mSphere Volume: 2 Issue: 2 Pages: 1-19
  • DOI: 10.1128/msphere.00359-16
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A Ralstonia solanacearum phage phiRP15 is closely related to Viunalikeviruses and encodes 19 tRNA-related sequences (2016)
  • Author(s): Tomoko Mihara, Mohamed A. Nasr-Eldin, Orawan Chatchawankanphanich, Anjana Bhunchoth, Namthip Phironrit, Takeru Kawasaki, Miyako Nakano, Makoto Fujie, Hiroyuki Ogata, Takashi Yamada
  • Journal Title: Virology Reports Volume: 6 Pages: 61-73
  • DOI: 10.1016/j.virep.2016.07.001
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Two Asian jumbo phages, phiRSL2 and phiRSF1, infect Ralstonia solanacearum and show common features of phiKZ-related phages (2016)
  • Author(s): Anjana Bhunchoth 他12名
  • Journal Title: Virology Volume: 494 Pages: 56-66
  • DOI: 10.1016/j.virol.2016.03.028
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Plankton networks driving carbon export in the oligotrophic ocean. (2016)
  • Author(s): Guidi L., Chaffron S., Bittner L., ..., Ogata H., ..., Karsenti E., Bowler C., Gorsky G.
  • Journal Title: Nature Volume: - Issue: 7600 Pages: 465-470
  • DOI: 10.1038/nature16942
  • NAID: 120005745631
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. (2016)
  • Author(s): Lescot M., Hingamp P., Kojima K.K., Villar E., Romac S., Veluchamy A., Boccara M., Jaillon O., Iudicone D., Bowler C., Wincker P., Claverie J.-M., Ogata H.
  • Journal Title: ISME J. Volume: 10 Issue: 5 Pages: 1134-1146
  • DOI: 10.1038/ismej.2015.192
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] DNA repair genes in the Megavirales pangenome. (2016)
  • Author(s): Blanc-Mathieu R., Ogata H.
  • Journal Title: Curr. Opin. Microbiol. Volume: 31 Pages: 94-100
  • DOI: 10.1016/j.mib.2016.03.011
  • NAID: 120005741090
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Linking virus genomes with host taxonomy. (2016)
  • Author(s): Mihara T., Nishimura Y., Shimizu Y., Nishiyama H., Yoshikawa G., Uehara H., Hingamp P., Goto S, Ogata H.
  • Journal Title: Viruses Volume: 8 Issue: 3 Pages: 66-66
  • DOI: 10.3390/v8030066
  • NAID: 120005947134
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The 474-kilobase-pair complete genome sequence of CeV-01B, a virus infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). (2015)
  • Author(s): Gallot-Lavallee L., Pagarete A., Legendre M., Santini S., Sandaa R.-A., Himmelbauer H., Ogata H., Bratbak G., Claverie J.-M.
  • Journal Title: Genome Announc. Volume: 3 Issue: 6
  • DOI: 10.1128/genomea.01413-15
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses. (2015)
  • Author(s): Takemura M., Yokobori S., Ogata H.
  • Journal Title: J. Mol. Evol. Volume: 81 Issue: 1-2 Pages: 24-33
  • DOI: 10.1007/s00239-015-9690-z
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Patterns and ecological drivers of ocean viral communities. (2015)
  • Author(s): Brum J.R., Ignacio-Espinoza J.C., Roux S., ..., Ogata H., ..., Wincker P., Karsenti E., Sullivan M.B.
  • Journal Title: Science Volume: 348 Issue: 6237 Pages: 6237-6237
  • DOI: 10.1126/science.1261498
  • NAID: 120005608041
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] 巨大ウイルスがもたらしたパンドラの箱 (2014)
  • Author(s): 緒方博之, 武村政春
  • Journal Title: 生物の科学 遺伝 Volume: 68 Pages: 194-199
• [Presentation] 遺伝子科学の昨今、生物学からのアプローチ. (2016)
  • Author(s): 緒方博之
  • Organizer: 2016年度日仏会館科学シンポジウム「遺伝子の科学」
  • Place of Presentation: 日仏会館ホール
  • Year and Date: 2016-12-03
  • Invited
• [Presentation] Extreme diversity, high abundance and activities of giant viruses in the sea. (2016)
  • Author(s): Ogata H.
  • Organizer: 日本分子生物学会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2016-12-02
• [Presentation] アメーバウイルス研究がもたらしたンパクト. (2016)
  • Author(s): 緒方博之
  • Organizer: 日本微生物生態学会年会
  • Place of Presentation: 横須賀
  • Year and Date: 2016-10-24
• [Presentation] あなたのウイルスゲノムを分類します. (2016)
  • Author(s): 西村陽介, 吉田天士, 緒方博之, 五斗進
  • Organizer: 日本微生物生態学会年会
  • Place of Presentation: 横須賀
  • Year and Date: 2016-10-23
• [Presentation] Tara Oceans expedition and giant viruses in marine ecosystems. (2016)
  • Author(s): Ogata H.
  • Organizer: Biodiversity and Chemical Biology of Marine and Terrestrial Life in the Philippine Region
  • Place of Presentation: Bohol, Philippines
  • Year and Date: 2016-10-17
  • Int'l Joint Research / Invited
• [Presentation] ウイルスは生命か？－巨大ウイルスを中心に－. (2016)
  • Author(s): 緒方博之
  • Organizer: 第56回生物物理若手の会夏の学校
  • Place of Presentation: 支笏湖ユースホステル
  • Year and Date: 2016-09-04
  • Invited
• [Presentation] 海洋巨大ウイルスの多様性と宿主予測. (2016)
  • Author(s): 緒方博之
  • Organizer: 水圏微生物研究フォーラム
  • Place of Presentation: 東京大学大気海洋研究所
  • Year and Date: 2016-08-09
  • Invited
• [Presentation] Virus-host database: a manually curated resource for viral host prediction. (2016)
  • Author(s): Mihara T., Nishimura Y., Nishiyama H., Goto S., Ogata H.
  • Organizer: 8th Aquatic Virus Workshop
  • Place of Presentation: Plymouth
  • Year and Date: 2016-07-13
  • Int'l Joint Research
• [Presentation] 海洋ウイルス 環境ゲノムから見る多様性・相互作用・分布 (2016)
  • Author(s): 緒方博之
  • Organizer: 日本海洋学会春季大会
  • Place of Presentation: 東京
  • Year and Date: 2016-03-17
  • Invited
• [Presentation] Assessing the diversity of the Megaviridae giant viruses based on RNA polymerase beta genes. (2015)
  • Author(s): Mihara T., Koyano H., Hingamp P., Goto S., Ogata H.
  • Organizer: Informatics in Biology, Medicine and Pharmacology 2015
  • Place of Presentation: 宇治
  • Year and Date: 2015-10-30
• [Presentation] Revealing complete genomes from metagenomes: a case study for viruses in the ocean. (2015)
  • Author(s): Nishimura Y., Watai W., Honda T., Omae K., Mihara T., Hingamp P., Yamamoto K., Sako Y., Yoshida T., Goto S., Ogata H.
  • Organizer: Informatics in Biology, Medicine and Pharmacology 2015
  • Place of Presentation: 宇治
  • Year and Date: 2015-10-29
• [Presentation] A GenomeNet resource for virus-host interaction network analyses. (2015)
  • Author(s): Mihara T., Nishimura Y., Uehara H., Hingamp P., Goto S., Ogata H.
  • Organizer: Annual meeting of Japanese Society of Microbial Ecology, 2015
  • Place of Presentation: 土浦
  • Year and Date: 2015-10-18
• [Presentation] A viral proteomic tree server and its application to a marine metagenomic study. (2015)
  • Author(s): Nishimura Y., Mihara T., Yoshida T., Hingamp P., Ogata H., Goto S
  • Organizer: Annual meeting of Japanese Society of Microbial Ecology, 2015
  • Place of Presentation: 土浦
  • Year and Date: 2015-10-18
• [Presentation] Metagenomic analysis of viral communities in Osaka bay, Japan. (2015)
  • Author(s): Watai H., Nishimura Y., Mihara T., Honda T, Yamamoto K, Hingamp P., Goto S., Ogata H., Sako Y, Yoshida T.
  • Organizer: Annual meeting of Japanese Society of Microbial Ecology, 2015
  • Place of Presentation: 土浦
  • Year and Date: 2015-10-18
• [Presentation] Diversity of marine giant DNA viruses. (2015)
  • Author(s): Mihara T., Koyano H., Goto S., Ogata H.
  • Organizer: International Workshop on Bioinformatics and Systems Biology 2015
  • Place of Presentation: Boston
  • Year and Date: 2015-07-19
  • Int'l Joint Research
• [Presentation] 巨大ウイルスは海洋生態系進化の原動力である (2014)
  • Author(s): 緒方博之
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2014-11-25 – 2014-11-27
• [Presentation] Why do some viruses encode amino acid biosynthetic genes? (2014)
  • Author(s): Mihara T., Goto S., Ogata H.
  • Organizer: 生命医薬情報学連合大会 2014
  • Place of Presentation: 仙台国際センター
  • Year and Date: 2014-10-02 – 2014-10-04
• [Remarks] Virus-Host Database
  • URL: http://www.genome.jp/virushostdb/
• [Remarks] ViPTree
  • URL: http://www.genome.jp/viptree/
• [Remarks] Taxonomy summary
  • URL: http://www.genome.jp/tools-bin/taxsummary
• [Remarks] MGENES
  • URL: http://www.genome.jp/mgenes/
• [Remarks] ウイルス―宿主データベース
  • URL: http://www.genome.jp/virushostdb/