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

• Project/Area Number: 23K25049
• Project/Area Number (Other): 22H03795 (2022-2023)
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Multi-year Fund (2024); Single-year Grants (2022-2023)
• Section: 一般
• Review Section: Basic Section 64040:Social-ecological systems-related
• Research Institution: Okinawa Institute of Science and Technology Graduate University
• Principal Investigator: 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)
• Project Period (FY): 2022-04-01 – 2025-03-31
• Project Status: Granted (Fiscal Year 2024)
• Budget Amount: ¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000); Fiscal Year 2024: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2023: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2022: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
• Keywords: Bioinformatics / Genomics / Climate change / Marine biology / Plankton / genomics / climate change / marine biology / plankton / bioinformatics

Outline of Research at the Start

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.

Outline of Annual Research Achievements

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.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

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.

Strategy for Future Research Activity

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.

Research Products

• [Int'l Joint Research] University of Barcelona(スペイン)
• [Journal Article] Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. (2024)
  • Author(s): 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.
  • Journal Title: Genome Research Volume: in press Pages: 426-440
  • DOI: 10.1101/gr.278295.123
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis (2023)
  • Author(s): Mahmoud-Reza Rafiee, Sara Rohban, Karen Davey, Jernej Ule, Nicholas M Luscombe
  • Journal Title: OXFORD Academic BRAIN Volume: 146 Issue: 6 Pages: 2547-2556
  • DOI: 10.1093/brain/awad046
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Clipplotr-a comparative visualization and analysis tool for CLIP data (2023)
  • Author(s): Anob M Chakrabarti, Charlotte Capitanchik, Jernej Ule, Nicholas M Luscombe
  • Journal Title: RNA Volume: 29 Pages: 715-723
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3 (2023)
  • Author(s): Anob M Chakrabarti, Ira A Iosub, Flora CY Lee, Jernej Ule, Nicholas M Luscombe
  • Journal Title: OXFORD University Press Volume: 51 Issue: 8 Pages: 3573-3589
  • DOI: 10.1093/nar/gkad221
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis (2023)
  • Author(s): Charlotte West, Charlotte Capitanchik, Chris Cheshire, Nicholas M Luscombe, Anob Chakrabarti, Jernej Ule
  • Journal Title: Wellcome Open Research Volume: 8 Pages: 286-286
  • DOI: 10.12688/wellcomeopenres.19453.1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale (2023)
  • Author(s): 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
  • Journal Title: bioRxiv, Cold Spring Harbor Lab Volume: -
  • DOI: 10.1101/2023.08.22.544179
  • Open Access / Int'l Joint Research
• [Journal Article] Poised PABP-RNA hubs implement signal-dependent mRNA decay in development (2023)
  • Author(s): 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
  • Journal Title: Research Gate Volume: -
  • DOI: 10.21203/rs.3.rs-3227673/v1
  • Open Access / Int'l Joint Research
• [Journal Article] scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border (2023)
  • Author(s): Alexandre P Thiery, Ailin Leticia Buzzi, Eva Hamrud, Chris Cheshire, Nicholas M Luscombe, James Briscoe, Andrea Streit
  • Journal Title: Elife Sciences Publications Limited Volume: 12
  • DOI: 10.7554/elife.82717
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains (2023)
  • Author(s): 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
  • Journal Title: Nature Communications Volume: - Pages: 5475-5475
  • Open Access / Int'l Joint Research
• [Journal Article] The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe. (2022)
  • Author(s): 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
  • Journal Title: Marine Biology Volume: 169 Issue: 12
  • DOI: 10.1007/s00227-022-04145-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Genomic scramble in marine plankton (2024)
  • Author(s): Nicholas M. Luscombe
  • Organizer: OIST x Kyudai Joint Symposium Series 1
• [Presentation] Targeted haplotype-aware assembly of complex regions and small genomes with NOVOLoci (2023)
  • Author(s): Nicolas Dierckxsens
  • Organizer: 14th AGW International Workshop
  • Int'l Joint Research
• [Presentation] Population Genomic Study Reveals Local Adaption Signals in Oikopleura dioica around Ryukyu Islands (2023)
  • Author(s): Jiashun Miao
  • Organizer: Tohoku International Symposium "Past, Present, and Future of the Marine Environment and Ecosystems"
  • Int'l Joint Research
• [Presentation] The species concept in environmental and genetic studies: the case of the zooplankton Oikopleura dioica going from global to cryptic (2023)
  • Author(s): Charles Plessy
  • Organizer: Tohoku International Workshop “Pathways Towards an Integrated Understanding of the Marine Environment and Marine Ecosystems”
  • Int'l Joint Research
• [Presentation] "Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica (2023)
  • Author(s): Michael Mansfield
  • Organizer: Keystone Symposium: Epigenetics, Chromatin, Development, and Disease. Vancouver, Canada
  • Int'l Joint Research
• [Presentation] Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe (2022)
  • Author(s): Aki Masunaga
  • Organizer: 11th International Tunicate Meeting (Kobe, Japan)
  • Int'l Joint Research
• [Presentation] Drastic genome remodeling across Oikopleura dioica worldwide (2022)
  • Author(s): Charles Plessy
  • Organizer: 11th International Tunicate Meeting (Kobe, Japan)
  • Int'l Joint Research
• [Presentation] Gene expression in the context of genomic rearrangement in Oikopleura dioica (2022)
  • Author(s): Michael Mansfield
  • Organizer: 11th International Tunicate Meeting (Kobe, Japan)
  • Int'l Joint Research
• [Presentation] Massively scrambled genomes producing animals with conserved morphology (2022)
  • Author(s): Charles Plessy
  • Organizer: 45th Annual Meeting of the Molecular Biology Society of Japan (Chiba, Japan)
  • Int'l Joint Research
• [Presentation] Related animals with small genomes, conserved morphology, but flexible gene order: Oikopleura dioica (2022)
  • Author(s): Charles Plessy
  • Organizer: Oceans - and the impact of humans and climate change - OIST-Tohoku U. 2nd Joint Workshop on Marine Science
• [Presentation] Uncovering speciation and population structures in the marine zooplankton, Oikopleura dioica (2022)
  • Author(s): Aki Masunaga
  • Organizer: Oceans - and the impact of humans and climate change - OIST-Tohoku U. 2nd Joint Workshop on Marine Science
• [Presentation] Drastic genome remodeling across Oikopleura dioica worldwide (2022)
  • Author(s): Charles Plessy
  • Organizer: Konan University Department of Biology Seminar. Kobe, Japan
  • Invited
• [Presentation] "Molecular clock estimation of divergence times in populations of "Oikopleura dioica" (2022)
  • Author(s): Michael Mansfield
  • Organizer: Oceans - and the impact of humans and climate change. Onna-son, Japan
• [Presentation] "Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica" (2022)
  • Author(s): Michael Mansfield
  • Organizer: Konan University Department of Biology Seminar. Kobe, Japan
  • Invited
• [Remarks] 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