Development of horizontal gene transfer detection system and elucidation of environmental adaptation and co-evolution process
| Project/Area Number |
17K00401
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Life / Health / Medical informatics
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| Research Institution | Niigata University |
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Principal Investigator |
Abe Takashi 新潟大学, 自然科学系, 教授 (30390628)
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| Co-Investigator(Kenkyū-buntansha) |
池村 淑道 長浜バイオ大学, バイオサイエンス学部, 客員教授 (50025475)
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| Project Period (FY) |
2017-04-01 – 2021-03-31
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| Project Status |
Completed (Fiscal Year 2020)
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| Budget Amount *help |
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
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| Keywords | 一括学習型自己組織化マップ / 連続塩基組成 / 水平伝播遺伝子 / 環境適応 / 共生細菌 / 系統推定 / 水平伝播候補遺伝子 / 南極細菌 / BLSOM / SC-BLSOM |
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| Outline of Final Research Achievements |
Horizontal gene transfer (HGT) has been searched by amino acid sequence similarity search, but only some genes could be detected. A comprehensive HGTs detection method for all genes on the genome is required. Focusing only on the oligonucleotide composition, we have developed a method for detecting candidate genes for HGTs and estimating its origin using a batch learning self-organizing map that can classify genome sequence fragments by biological type with high accuracy. As an application, analysis of two species of Sphingomonas spp. derived from Antarctic moss showed that the origin of HGT gene was significantly different, but the HGT gene functions were common. The development method is useful not only for detecting HGT candidates and their origins throughout the genome, but also as a method that can provide a new perspective on the environmental adaptation of microorganisms.
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| Academic Significance and Societal Importance of the Research Achievements |
生物の進化や環境適応には生物種間での遺伝子の水平伝播が大きな役割を果たしている．配列相同性検索などの従来手法では水平伝播遺伝子の検出精度に限界があったが，本研究にて開発した水平伝播予測ワークフローは，ゲノム全体における水平伝播遺伝子の全容解明を可能とした．南極由来細菌の異なる系統の同属異種間における水平伝播遺伝子探索を行ったところ，水平伝播で獲得した遺伝子の機能やアミノ酸組成の変化など多くの共通した特徴が見られ，南極環境に適応するプロセスにおいて収斂進化の可能性が示唆された．様々な環境下での生育環境適応戦略や共生関係が及ぼしてきた共進化過程の解明への活用が期待できる．
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Report
(5 results)
Research Products
(19 results)
