2020 Fiscal Year Annual Research Report
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 Institution | Okinawa Institute of Science and Technology Graduate University |
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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)
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| 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
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| Project Period (FY) |
2020-09-25 – 2022-03-31
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| Keywords | genomics / bioinformatics / marine biology / zooplankton / Oikopleura / functional genomics / ecology / evolution |
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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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[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
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
Pages: -
DOI
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
ERJ open research
Volume: 6
Pages: -
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis2020
Author(s)
Eckhard, U., Bloechl, C., Jenkins, B. G., Mansfield, M. J., Huber, C. G., Doxey, A. C., & Brandstetter, H.
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Journal Title
Scientific reports
Volume: 10
Pages: 1-13
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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