Development of coral reef monitoring method using environmental DNA technology

• Project/Area Number: 17K07949
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Aquatic life science
• Research Institution: The University of Tokyo
• Principal Investigator: Shinzato Chuya 東京大学, 大気海洋研究所, 准教授 (70524726)
• Co-Investigator(Kenkyū-buntansha): 鈴木 豪 国立研究開発法人水産研究・教育機構, 水研機構(長崎), 主任研究員 (30533319)
• Project Period (FY): 2017-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2019: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000); Fiscal Year 2018: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: サンゴ / 環境DNA / 褐虫藻 / ゲノム

Outline of Final Research Achievements

The situation of coral reefs is becoming more serious due to climate change etc., and it is important to monitor them closely. In this study, we focused on environmental DNA in seawater and aimed to develop a new monitoring method that would enable us to detect corals simply by pumping seawater. Tank experiments were conducted to confirm whether corals and symbiotic algae could be detected in seawater, and the results showed that environmental DNA in seawater reflects well the status of corals in the vicinity

Academic Significance and Societal Importance of the Research Achievements

海水中の環境DNAは近傍に存在するサンゴの状況を反映しているのか、太平洋・インド洋の代表的な造礁サンゴであるミドリイシ属を用いて、水槽実験を行い検証した。実験に使用した全てのサンゴ、共生している共生藻類のDNA配列タイプを、海水中から検出することができた。水槽飼育したサンゴ由来の環境DNAは、それぞれのサンゴの水中重量・種組成と相関していることから、環境DNAを用いたサンゴのモニタリングは可能であると考えられる。

Research Products

• [Journal Article] Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera (2020)
  • Author(s): Shoguchi Eiichi、Yoshioka Yuki、Shinzato Chuya、Arimoto Asuka、Bhattacharya Debashish、Satoh Noriyuki
  • Journal Title: Genome Biology and Evolution Volume: 12 Issue: 3 Pages: 203-209
  • DOI: 10.1093/gbe/evaa042
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis (2020)
  • Author(s): Chiu Yi-Ling、Shikina Shinya、Yoshioka Yuki、Shinzato Chuya、Chang Ching-Fong
  • Journal Title: BMC Genomics Volume: 21 Issue: 1
  • DOI: 10.1186/s12864-020-07113-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [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] Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral?Algae Symbioses (2020)
  • Author(s): Yoshioka Yuki、Yamashita Hiroshi、Suzuki Go、Zayasu Yuna、Tada Ipputa、Kanda Miyuki、Satoh Noriyuki、Shoguchi Eiichi、Shinzato Chuya
  • Journal Title: Genome Biology and Evolution Volume: 13 Issue: 1 Pages: 1-18
  • DOI: 10.1093/gbe/evaa240
  • Peer Reviewed / Open Access
• [Journal Article] Discovery of a receptor guanylate cyclase expressed in the sperm flagella of stony corals (2019)
  • Author(s): Zhang Y, Chiu YL, Chen CJ, Ho YY, Shinzato C, Shikina S, Chang CF.
  • Journal Title: Scientific reports Volume: 9 Issue: 1 Pages: 1-9
  • DOI: 10.1038/s41598-019-51224-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Warm seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea (2019)
  • Author(s): Guzman C, Atrigenio M, Shinzato C, Alino P, Conaco C.
  • Journal Title: PeerJ Volume: e7785 Pages: e7785-e7785
  • DOI: 10.7717/peerj.7785
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Siphonous Macroalgal Genome Suggests Convergent Functions of Homeobox Genes in Algae and Land Plants (2019)
  • Author(s): Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E.
  • Journal Title: DNA Research Volume: 26 Issue: 2 Pages: 183-192
  • DOI: 10.1093/dnares/dsz002
  • Peer Reviewed / Open Access
• [Journal Article] Medusozoan genomes inform the evolution of the jellyfish body plan (2019)
  • Author(s): Khalturin K, Shinzato C, Khalturina M, Hamada M, Fujie M, Koyanagi 5, Kanda M, Goto H, Anton-Erxleben F, Toyokawa M, Toshino S, Satoh N
  • Journal Title: Nature Ecology and Evolution Volume: 3(5) Issue: 5 Pages: 811-822
  • DOI: 10.1038/s41559-019-0853-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Symbiosis process between Acropora larvae and Symbiodinium differs even among closely related Symbiodinium types (2018)
  • Author(s): Yamashita H、Suzuki G、Shinzato C、Jimbo M、Koike K
  • Journal Title: Marine Ecology Progress Series Volume: 592 Pages: 119-128
  • DOI: 10.3354/meps12474
  • Peer Reviewed
• [Journal Article] Genetic diversity of farmed and wild populations of the reef-building coral, Acropora tenuis (2018)
  • Author(s): Zayasu Yuna、Satoh Noriyuki、Shinzato Chuya
  • Journal Title: Restoration Ecology Volume: 印刷中 Issue: 6 Pages: 1195-1202
  • DOI: 10.1111/rec.12687
  • Peer Reviewed / Open Access
• [Journal Article] Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA (2018)
  • Author(s): Shinzato C, Zayasu Y, Kanda M, Kawamitsu M, Satoh N, Yamashita H and Suzuki G
  • Journal Title: Frontiers in Marine Science Volume: 5 Pages: 28-28
  • DOI: 10.3389/fmars.2018.00028
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Using genomics to reveal novel insights into coral biology (2021)
  • Author(s): Chuya Shinzato
  • Organizer: Genome Concept Centennial Conference
  • Int'l Joint Research / Invited
• [Presentation] 有藻性サンゴ、ミドリイシ属の種判別遺伝子マーカー開発の取組み (2021)
  • Author(s): 村山昌、座安佑奈、鈴木豪、新里宙也
  • Organizer: 令和3年度日本水産学会春季大会
• [Presentation] 18種のミドリイシ科サンゴの全ゲノム解読が明らかにする，ミドリイシ属の環境適応戦略 (2020)
  • Author(s): 新里宙也，Konstantin Khalturin，井上潤，座安佑奈，神田美幸，川満真由美，善岡祐輝，山下洋，鈴木豪，佐藤矩行
  • Organizer: 日本サンゴ礁学会第23回大会
• [Presentation] 高精度な比較ゲノムを可能とするミドリイシ科サンゴからの遺伝子モデル構築 (2020)
  • Author(s): 善岡祐輝、山下洋、鈴木豪、新里 宙也
  • Organizer: 日本サンゴ礁学会第23回大会
• [Presentation] 造礁サンゴ、コユビミドリイシのゲノムワイドSNPを用いた、南西諸島における集団構造解析 (2020)
  • Author(s): 土屋考人、座安佑奈、中島祐一、鈴木豪、佐藤矩行、新里宙也
  • Organizer: 日本サンゴ礁学会第23回大会
• [Presentation] サンゴ特異的 Notch 様遺伝子が、褐虫藻との共生関係を制御している ? (2019)
  • Author(s): 善岡祐輝、山下洋、邱顗陵、蔡品萱、座安佑奈、鈴木豪、識名信也、新里宙也
  • Organizer: 日本サンゴ礁学会第22回大会
• [Presentation] Durusdinium属褐虫藻とAcropora tenuis 幼生の初期共生 (2019)
  • Author(s): 山下 洋，鈴木 豪，新里 宙也，善岡 祐輝
  • Organizer: 日本サンゴ礁学会第22回大会
• [Presentation] Application of genomics to coral biology (2018)
  • Author(s): Chuya Shinzato
  • Organizer: 6th Taiwan-Japan Ecology Workshop
  • Int'l Joint Research / Invited
• [Presentation] Conservation and restoration of coral reefs: the most diverse marine ecosystems (2018)
  • Author(s): Chuya Shinzato
  • Organizer: 5th Asian conference on Safety and Education in Laboratory
  • Int'l Joint Research / Invited
• [Presentation] Coral genome project for understanding the most diverse of all marine ecosystems (2018)
  • Author(s): Chuya Shinzato
  • Organizer: 1st Korea-Japan (OIST) Joint International Symposium on Marine Genomics
  • Int'l Joint Research / Invited
• [Presentation] Genomics approaches for investigating probable cross-talk between coral and algae (2018)
  • Author(s): Chuya Shinzato
  • Organizer: ARC CoE Boden Research Conference “Origins and Function of Animal Metaorganism”, Townsville, Australia
  • Int'l Joint Research / Invited
• [Presentation] ゲノム科学的手法による造礁サンゴの遺伝的多様性の理解 (2017)
  • Author(s): 新里宙也
  • Organizer: 日本動物学会 第36回ホヤの生物学談話会
  • Invited
• [Presentation] ゲノム科学的手法によるサンゴ共生系の理解 (2017)
  • Author(s): 新里宙也
  • Organizer: 第1回日本共生生物学会大会
  • Invited