The development of computational pipeline for species discovery and diversity analysis of fishes detected from environmental water DNA
| Project/Area Number |
15K18590
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Biodiversity/Systematics
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| Research Institution | University of the Ryukyus (2016)
Tohoku University (2015) |
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Principal Investigator |
SATO Yukuto 琉球大学, 戦略的研究プロジェクトセンター, 特命講師 (20566418)
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| Project Period (FY) |
2015-04-01 – 2017-03-31
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| Project Status |
Completed (Fiscal Year 2016)
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| Budget Amount *help |
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
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| Keywords | 環境DNA / 魚類 / 脊椎動物 / 次世代シークエンサー / ビッグデータ / 解析パイプライン / 環境生態 / ミトコンドリアDNA / メタバーコーディング |
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| Outline of Final Research Achievements |
The computational pipeline was developed to comprehensively identify the animal and/or fish species based on DNA analysis of environmental water samples from sea, river, etc. The pipeline conducts animal metabarcoding analysis using partial mitochondrial 12S rRNA gene (170 bp) amplified from fish- and animal-related water suspensions, in which the quality filtering and the Blast-based species assignment of more than ten million sequences were automated. In addition, the pipeline enables LOD score-based evaluation of species assignment results and automatic generation of molecular phylogenetic trees that would be useful for analysis of ecological diversity and discovery of new species.
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Report
(3 results)
Research Products
(3 results)
