| Project/Area Number |
22KF0418
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| Project/Area Number (Other) |
22F22379 (2022)
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| Research Category |
Grant-in-Aid for JSPS Fellows
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| Allocation Type | Multi-year Fund (2023)
Single-year Grants (2022) |
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| Section | 外国 |
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| Review Section |
Basic Section 45020:Evolutionary biology-related
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| Research Institution | Japan Agency for Marine-Earth Science and Technology (2023)
National Institute of Advanced Industrial Science and Technology (2022) |
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Principal Investigator |
延 優 (NOBUMASARU・KONISHI) 国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(超先鋭研究開発プログラム), 主任研究員 (40805644)
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| Co-Investigator(Kenkyū-buntansha) |
MEI RAN 国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(超先鋭研究開発プログラム), 外国人特別研究員
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| Project Period (FY) |
2023-03-08 – 2025-03-31
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| Project Status |
Granted (Fiscal Year 2023)
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| Budget Amount *help |
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 2024: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 2023: ¥500,000 (Direct Cost: ¥500,000)
Fiscal Year 2022: ¥1,100,000 (Direct Cost: ¥1,100,000)
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| Keywords | Archaea / Genomics / Evolution / Bioinformatics / Genes |
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| Outline of Research at the Start |
We have massive amounts of genomic insight into life on Earth, yet the data remains challenging to explore due to the lack of organization - only a small fraction of genes have known biochemical function. However, we need not know genes’ functions to extract useful information. One approach to explore genetic space is combination of cutting-edge gene clustering algorithms and evolution reconstruction tools.
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| Outline of Annual Research Achievements |
Based on the clustering of genes from all publicly available archaea genomes into homologous groups using the workstation purchased with this grant, we reconstructed the evolutionary history of nearly half of the protein groups. This was performed through construction of rooted phylogenetic trees for each protein group and estimation of the simplest evolutionary scheme using these gene trees, a tree of life spanning all analyzed genomes, and duplication, transfer, and loss reconciliation. In doing so, the origin of each protein group and which lineages vertically or horizontally inherited or lost the functions could be predicted.
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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
Tree estimation and duplication, transfer, loss reconciliation are time-consuming but in-house approaches for reducing calculation times allowed for rapid analysis.
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| Strategy for Future Research Activity |
Phylogenetic analyses of the remaining protein groups will be completed in the early half of the 2024 fiscal year. With a holistic view of the evolution of functions across the tree of archaeal life, we can begin to reconstruct the evolutionary background and relationships behind contemporary and ancient lifestyles. The obtained detailed evolutionary view of archaea will also be used to provide quantitative data regarding the evolution of archaea. The duplication, transfer, and loss rates in bacteria have been explored, but data/analyses remain scarce for archaea. Without such information, the fundamental evolutionary characteristics of the two domains of prokaryotic life cannot be compared. Here, in the following months, we aim to complete such a comparison to provide a clear view of the evolutionary differences between the two domains.
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