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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
Host Researcher 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)
Foreign Research Fellow 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 Granted (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 FY2020, I published several works related to my PhD. The most important is an online database and classification scheme for the toxins of Clostridioides difficile. I contributed to two articles on SARS-CoV-2, the virus that causes COVID-19. In one paper, we demonstrated that the virus' proposed receptor is expressed very little in the human airway.

For my postdoctoral research, our lab completed several key milestones: we published an initial assembly for the Okinawan Oikopleura dioica genome in BMC Genomics; using Nanopore and Illumina sequencing, we have produced a haplotype-resolved genome for the Okinawan species; we have produced genome assemblies from PacBio HiFi data; and, we have started development of a computational pipeline for genome assembly and annotation.

Current Status of Research Progress
Current Status of Research Progress

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

Reason

A major goal for FY2020 was to produce a haplotype-resolved genome for the Okinawa Oikopleura. We have succeeded in this. We have also succeeded in using the PacBio HiFi platform to sequence individual Oikopleura.

In the last year we have created a tool to assemble and annotate eukaryotic genomes. We are now developing a generalized method to automate these for other genomics researchers, which we will contribute to the nf-core open-source collaborative project.

We have successfully established the ATACseq protocol in Okinawan Oikopleura. We have created a robust experimental design for comparing functional genomics measurements from several Oikopleura species, and will collect and analyze these data by the end of the year, to be published before FY2022.

Strategy for Future Research Activity

One goal of the project for FY2021 is to complete the analysis of our haplotype-resolved Oikopleura genomes. A few tasks remain to be done to complete this part of the project, but they should be completed in a few months.

We will continue development of our genome assembly and annotation pipeline, which we will contribute to nf-core before 2022.

The major goal for the second half of FY2021 is to produce and analyze functional genomics data for multiple species of Oikopleura. This involves acquiring and culturing the animals at our facilities at OIST. Once we have obtained stable cultures of the animals, we will measure changes in gene expression throughout development.

Report

(1 results)
  • 2020 Annual Research Report

Research Products

(6 results)

All 2021 2020

All Journal Article (6 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 6 results,  Open Access: 5 results)

  • [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 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

    • 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

    • 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 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

      Scientific reports

      Volume: 6 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

    • DOI

      10.1371/journal.ppat.1009181

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research

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Published: 2020-09-29   Modified: 2021-12-27  

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