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ユビキタス海洋動物プランクトン、ワカレオタマボヤの集団ゲノム科学

Research Project

Project/Area Number 20F20760
Research Category

Grant-in-Aid for JSPS Fellows

Allocation TypeSingle-year Grants
Section外国
Review Section Basic Section 43050:Genome biology-related
Research InstitutionOkinawa 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)

Co-Investigator(Kenkyū-buntansha) MANSFIELD MICHAEL  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, 外国人特別研究員
Project Period (FY) 2020-09-25 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥2,300,000 (Direct Cost: ¥2,300,000)
Fiscal Year 2021: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2020: ¥1,200,000 (Direct Cost: ¥1,200,000)
Keywordsgenomics / bioinformatics / marine biology / zooplankton / Oikopleura / functional genomics / ecology / evolution
Outline of Research at the Start

Larvaceans are a group of filter-feeding zooplankton found in all the world’s oceans, but surprisingly little is known about their population structure and genetic diversity. The larvacean that we most specialize in is Oikopleura dioica. It is one of the smallest larvaceans known - both in size and genetic composition - and its life cycle in the lab is only 4 days, making it an ideal model for our experiments. In our lab, we analyze the genetic information of O. dioica and other larvaceans and use this to understand how these mysterious organisms survive and evolve.

Outline of Annual Research Achievements

In FY2021, I contributed to two studies on genetic variation in O. dioica. The first reports that the species O. dioica may in fact be a species complex representing multiple lineages. The second demonstrates a considerable degree of genetic rearrangement in these species, which is unique among chordates and perhaps all metazoa.
We began follow-up studies to examine the effects of this rearrangement on gene expression, achieving two important milestones in FY2021. In FY2020, we established the ATACseq method. In FY2021 we completed sampling and sequencing for RNAseq and ATACseq in two O. dioica populations, across developmental time points. We also established the hybridization chain reaction in O. dioica to accurately observe the spatiotemporal patterns of expression in real time.

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (8 results)

All 2022 2021 2020

All Journal Article (7 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 7 results,  Open Access: 6 results) Presentation (1 results)

  • [Journal Article] Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold2022

    • Author(s)
      Sugiman-Marangos, S. N., Gill, S. K., Mansfield, M. J., Orrell, K. E., Doxey, A. C., & Melnyk, R. A.
    • Journal Title

      Communications biology

      Volume: 5(1) Issue: 1 Pages: 1-12

    • DOI

      10.1038/s42003-022-03333-9

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing2021

    • Author(s)
      Aleksandra Bliznina, Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Charlotte West, Tanmay Rustagi, Hsiao-Chiao Chien, Saurabh Kumar, Julien Pichon, Charles Plessy & Nicholas M. Luscombe
    • Journal Title

      BMC genomics

      Volume: 22 Issue: 1 Pages: 1-18

    • DOI

      10.1186/s12864-021-07512-6

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens.2020

    • Author(s)
      Briallen Lobb, Rhiannon Hodgson, Michael D. J. Lynch, Michael J. Mansfield, Jiujun Cheng, Trevor C. Charles, Josh D. Neufeld, Paul M. Craig, & Andrew C. Doxey
    • Journal Title

      MSystems

      Volume: 5 Issue: 2

    • DOI

      10.1128/msystems.00145-20

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue2020

    • Author(s)
      Aguiar,J.A.,Tremblay,B.J.,Mansfield,M.J.,Woody,O.,Lobb,B.,Banerjee,A.,...& Hirota,J.A
    • Journal Title

      European Respiratory Journal

      Volume: 56 Issue: 3 Pages: 2001123-2001123

    • DOI

      10.1183/13993003.01123-2020

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus.2020

    • Author(s)
      Arinjay Banerjee, Andrew C. Doxey, Benjamin J.-M. Tremblay, Michael J. Mansfield, Sonu Subudhi, Jeremy A. Hirota, Matthew S. Miller, Andrew G. McArthur, Samira Mubareka & Karen Mossman
    • Journal Title

      Journal of General Virology

      Volume: 101 Issue: 12 Pages: 1251-1260

    • DOI

      10.1099/jgv.0.001491

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status2020

    • Author(s)
      Matthew F. Fantauzzi, Jennifer A. Aguiar, Benjamin J.-M. Tremblay, Michael J. Mansfield, Toyoshi Yanagihara, Abiram Chandiramohan, Spencer Revill, Min Hyung Ryu, Chris Carlsten, Kjetil Ask, Martin Staempfli, Andrew C. Doxey & Jeremy A. Hirota
    • Journal Title

      ERJ open research

      Volume: 6 Issue: 1 Pages: 1-13

    • DOI

      10.1038/s41598-020-76010-8

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B.2020

    • Author(s)
      Michael J. Mansfield, Benjamin J-M Tremblay, Ji Zeng, Xin Wei, Harold Hodgins, Jay Worley, Lynn Bry, Min Dong, & Andrew C. Doxey
    • Journal Title

      PLoS pathogens

      Volume: 16 Issue: 12 Pages: e1009181-e1009181

    • DOI

      10.1371/journal.ppat.1009181

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Molecular clock estimation of divergence times in populations of Oikopleura dioica2022

    • Author(s)
      Michael Mansfield and the Luscombe Lab
    • Organizer
      OIST-Tohoku Marine Science Workshop
    • Related Report
      2021 Annual Research Report

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Published: 2020-09-29   Modified: 2024-03-26  

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