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

2023 年度 実績報告書

• 研究課題/領域番号: 22H03795
• 配分区分: 補助金
• 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
• キーワード: Bioinformatics / Genomics / Climate change / Marine biology / Plankton

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

• [雑誌論文] Extreme genome scrambling in cryptic Oikopleura dioica species (2024)
  • 著者名/発表者名: C.Plessy, M.J.Mansfield, A.Bliznina, A.Masunaga, C.West, Y.Tan, A.Liu, J.Grasic, M.S. del Rio Pisula, G.Sanchez-Serna, M.Fabrega-Torrus, A.Ferrnandez-Roldan, V.Roncalli, P.Navratilova, E.M.Thompson, T.Onuma, H.Nishida, C.Canestro, N.M.Luscombe
  • 雑誌名: Cold Spring Harbor Lab 巻: 34 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 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 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
  • 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: - ページ: -
  • 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: - ページ: -
  • 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 ページ: e82717
  • 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
  • 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
• [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