| 研究課題/領域番号 |
20F20760
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| 研究機関 | 沖縄科学技術大学院大学 |
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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)
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| 研究分担者 |
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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| 研究期間 (年度) |
2020-09-25 – 2022-03-31
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| キーワード | genomics / bioinformatics / marine biology / zooplankton / Oikopleura / functional genomics / ecology / evolution |
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| 研究実績の概要 |
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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| 現在までの達成度 (区分) |
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
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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| 今後の研究の推進方策 |
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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