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
| Project/Area Number |
20F20760
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| Research Category |
Grant-in-Aid for JSPS Fellows
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| Allocation Type | Single-year Grants |
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| Section | 外国 |
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| Review Section |
Basic Section 43050:Genome biology-related
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| Research Institution | Okinawa Institute of Science and Technology Graduate University |
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| 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)
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| 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
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| Project Period (FY) |
2020-09-25 – 2022-03-31
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| Project Status |
Granted (Fiscal Year 2021)
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| 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)
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| Keywords | genomics / bioinformatics / marine biology / zooplankton / Oikopleura / functional genomics / ecology / evolution |
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| 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.
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| 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.
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| 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.
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| 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.
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Report
(1 results)
Research Products
(6 results)
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[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
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Journal Title
BMC genomics
Volume: 22
Pages: 1-18
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[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
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Journal Title
European Respiratory Journal
Volume: 56
DOI
Related Report
Peer Reviewed / Int'l Joint Research
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[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
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Journal Title
Scientific reports
Volume: 6
Pages: 1-13
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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