Adaptation of marine zooplankton to climate change conditions: a multi-omic study of molecular mechanisms.

• 研究課題/領域番号: 23K25049
• 補助金の研究課題番号: 22H03795 (2022-2023)
• 研究種目: 基盤研究(B)
• 配分区分: 基金 (2024); 補助金 (2022-2023)
• 応募区分: 一般
• 審査区分: 小区分64040:自然共生システム関連
• 研究機関: 沖縄科学技術大学院大学
• 研究代表者: ラスカム ニコラス 沖縄科学技術大学院大学, ゲノム・遺伝子制御システム科学ユニット, 教授 (70724087)
• 研究期間 (年度): 2022-04-01 – 2025-03-31
• 研究課題ステータス: 交付 (2024年度)
• 配分額: 17,420千円 (直接経費: 13,400千円、間接経費: 4,020千円); 2024年度: 5,200千円 (直接経費: 4,000千円、間接経費: 1,200千円); 2023年度: 5,200千円 (直接経費: 4,000千円、間接経費: 1,200千円); 2022年度: 7,020千円 (直接経費: 5,400千円、間接経費: 1,620千円)
• キーワード: Bioinformatics / Genomics / Climate change / Marine biology / Plankton / genomics / climate change / marine biology / plankton / bioinformatics

研究開始時の研究の概要

The climate crisis is impacting marine ecosystems, notably affecting plankton like Oikopleura dioica, which thrives along Japan's coastline. Our study investigates how these zooplankton adapt by simulating climate change conditions, studying physiological responses, and analyzing genetic data. We aim to uncover molecular strategies that enable their survival in changing environments, providing insights into the adaptation mechanisms of marine chordates.

研究実績の概要

In the past 12 months, we have published a paper on the observation of large-scale genomic rearrangements between Oikopleura dioca populations, and demonstrated that the Okinawa population forms a distinct sub-species of Oikopleura, even though their appearance is near-identical to the mainland Japanese populations.

現在までの達成度 (区分)

2: おおむね順調に進展している

理由

The project has progressed as expected, with gene expression and chromatin status measurements for Okinawa and Osaka populations completed. We are now analysing the data, in order to understand the similarities and differences in the regulatory wiring of the two populations, at normal and at different environmental conditions.

今後の研究の推進方策

In the final year of project, we will focus on analysing the data, performing validation experiments, and writing a paper to be submitted in late 2024/early 2025.

研究成果

• [国際共同研究] University of Barcelona(スペイン)
• [雑誌論文] Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. (2024)
  • 著者名/発表者名: Plessy, C., Mansfield, M.J., Bliznina, A., Masunaga, A., West, C., Tan, Y., Liu, A.W., Grasic, J., Del Rio Pisula, M.S., Sanchez-Serna, G., Fabrega-Torrus, M., Ferrandez-Roldan, A., Roncalli, V., Navratilova, P., Thompson, E.M., Onuma, T., Nishida, H., Canestro, C., Luscombe, N.M.
  • 雑誌名: Genome Research 巻: in press ページ: 426-440
  • DOI: 10.1101/gr.278295.123
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis (2023)
  • 著者名/発表者名: Mahmoud-Reza Rafiee, Sara Rohban, Karen Davey, Jernej Ule, Nicholas M Luscombe
  • 雑誌名: OXFORD Academic BRAIN 巻: 146 号: 6 ページ: 2547-2556
  • DOI: 10.1093/brain/awad046
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] Clipplotr-a comparative visualization and analysis tool for CLIP data (2023)
  • 著者名/発表者名: Anob M Chakrabarti, Charlotte Capitanchik, Jernej Ule, Nicholas M Luscombe
  • 雑誌名: RNA 巻: 29 ページ: 715-723
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3 (2023)
  • 著者名/発表者名: Anob M Chakrabarti, Ira A Iosub, Flora CY Lee, Jernej Ule, Nicholas M Luscombe
  • 雑誌名: OXFORD University Press 巻: 51 号: 8 ページ: 3573-3589
  • DOI: 10.1093/nar/gkad221
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] Nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis (2023)
  • 著者名/発表者名: Charlotte West, Charlotte Capitanchik, Chris Cheshire, Nicholas M Luscombe, Anob Chakrabarti, Jernej Ule
  • 雑誌名: Wellcome Open Research 巻: 8 ページ: 286-286
  • DOI: 10.12688/wellcomeopenres.19453.1
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale (2023)
  • 著者名/発表者名: Charlotte Capitanchik, Sam Ireland, Alex Harston, Chris Cheshire, D Marc Jones, Flora CY Lee, Igor Ruiz de los Mozos, Ira A Iosub, Klara Kuret, Rupert Faraway, Oscar G Wilkins, Rahul Arora, Martina Hallegger, Miha Modic, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
  • 雑誌名: bioRxiv, Cold Spring Harbor Lab 巻: -
  • DOI: 10.1101/2023.08.22.544179
  • オープンアクセス / 国際共著
• [雑誌論文] Poised PABP-RNA hubs implement signal-dependent mRNA decay in development (2023)
  • 著者名/発表者名: Jernej Ule, Miha Modic, Klara Kuret, Sebastian Steinhauser, Rupert Faraway, Emiel van Genderen, Flora Lee, Igor Ruiz de Los Mozos, Ziga Vicic, Jona Novljan, Derk ten Berge, Nicholas Luscombe
  • 雑誌名: Research Gate 巻: -
  • DOI: 10.21203/rs.3.rs-3227673/v1
  • オープンアクセス / 国際共著
• [雑誌論文] scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border (2023)
  • 著者名/発表者名: Alexandre P Thiery, Ailin Leticia Buzzi, Eva Hamrud, Chris Cheshire, Nicholas M Luscombe, James Briscoe, Andrea Streit
  • 雑誌名: Elife Sciences Publications Limited 巻: 12
  • DOI: 10.7554/elife.82717
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains (2023)
  • 著者名/発表者名: Harold P Hodgins, Pengsheng Chen, Briallen Lobb, Xin Wei, Benjamin JM Tremblay, Michael J Mansfield, Victoria CY Lee, Pyung-Gang Lee, Jeffrey Coffin, Ana T Duggan, Alexis E Dolphin, Gabriel Renaud, Min Dong, Andrew C Doxey
  • 雑誌名: Nature Communications 巻: - ページ: 5475-5475
  • オープンアクセス / 国際共著
• [雑誌論文] The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe. (2022)
  • 著者名/発表者名: Masunaga A, Mansfield MJ, Tan Y, Liu AW, Bliznina A, Barzaghi P, Hodgetts TL, Ferrandez‐Roldan A, Canestro C, Onuma TA, Plessy C and Luscombe NM
  • 雑誌名: Marine Biology 巻: 169 号: 12
  • DOI: 10.1007/s00227-022-04145-5
  • 査読あり / オープンアクセス / 国際共著
• [学会発表] Genomic scramble in marine plankton (2024)
  • 著者名/発表者名: Nicholas M. Luscombe
  • 学会等名: OIST x Kyudai Joint Symposium Series 1
• [学会発表] Targeted haplotype-aware assembly of complex regions and small genomes with NOVOLoci (2023)
  • 著者名/発表者名: Nicolas Dierckxsens
  • 学会等名: 14th AGW International Workshop
  • 国際学会
• [学会発表] Population Genomic Study Reveals Local Adaption Signals in Oikopleura dioica around Ryukyu Islands (2023)
  • 著者名/発表者名: Jiashun Miao
  • 学会等名: Tohoku International Symposium "Past, Present, and Future of the Marine Environment and Ecosystems"
  • 国際学会
• [学会発表] The species concept in environmental and genetic studies: the case of the zooplankton Oikopleura dioica going from global to cryptic (2023)
  • 著者名/発表者名: Charles Plessy
  • 学会等名: Tohoku International Workshop “Pathways Towards an Integrated Understanding of the Marine Environment and Marine Ecosystems”
  • 国際学会
• [学会発表] "Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica (2023)
  • 著者名/発表者名: Michael Mansfield
  • 学会等名: Keystone Symposium: Epigenetics, Chromatin, Development, and Disease. Vancouver, Canada
  • 国際学会
• [学会発表] Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe (2022)
  • 著者名/発表者名: Aki Masunaga
  • 学会等名: 11th International Tunicate Meeting (Kobe, Japan)
  • 国際学会
• [学会発表] Drastic genome remodeling across Oikopleura dioica worldwide (2022)
  • 著者名/発表者名: Charles Plessy
  • 学会等名: 11th International Tunicate Meeting (Kobe, Japan)
  • 国際学会
• [学会発表] Gene expression in the context of genomic rearrangement in Oikopleura dioica (2022)
  • 著者名/発表者名: Michael Mansfield
  • 学会等名: 11th International Tunicate Meeting (Kobe, Japan)
  • 国際学会
• [学会発表] Massively scrambled genomes producing animals with conserved morphology (2022)
  • 著者名/発表者名: Charles Plessy
  • 学会等名: 45th Annual Meeting of the Molecular Biology Society of Japan (Chiba, Japan)
  • 国際学会
• [学会発表] Related animals with small genomes, conserved morphology, but flexible gene order: Oikopleura dioica (2022)
  • 著者名/発表者名: Charles Plessy
  • 学会等名: Oceans - and the impact of humans and climate change - OIST-Tohoku U. 2nd Joint Workshop on Marine Science
• [学会発表] Uncovering speciation and population structures in the marine zooplankton, Oikopleura dioica (2022)
  • 著者名/発表者名: Aki Masunaga
  • 学会等名: Oceans - and the impact of humans and climate change - OIST-Tohoku U. 2nd Joint Workshop on Marine Science
• [学会発表] Drastic genome remodeling across Oikopleura dioica worldwide (2022)
  • 著者名/発表者名: Charles Plessy
  • 学会等名: Konan University Department of Biology Seminar. Kobe, Japan
  • 招待講演
• [学会発表] "Molecular clock estimation of divergence times in populations of "Oikopleura dioica" (2022)
  • 著者名/発表者名: Michael Mansfield
  • 学会等名: Oceans - and the impact of humans and climate change. Onna-son, Japan
• [学会発表] "Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica" (2022)
  • 著者名/発表者名: Michael Mansfield
  • 学会等名: Konan University Department of Biology Seminar. Kobe, Japan
  • 招待講演
• [備考] Species identity crisis in the genome community
  • URL: https://www.oist.jp/news-center/news/2024/5/9/oikopleura-who-species-identity-crisis-genome-community