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The development of computational pipeline for species discovery and diversity analysis of fishes detected from environmental water DNA

Research Project

Project/Area Number 15K18590
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biodiversity/Systematics
Research InstitutionUniversity of the Ryukyus (2016)
Tohoku University (2015)

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)

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
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)
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
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.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (3 results)

All 2017 2016 2015

All Journal Article (2 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Book (1 results)

  • [Journal Article] Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea2017

    • Author(s)
      Yamamoto, Masuda, Sato, Sado, Araki, Kondoh, Minamoto, Miya
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 40368-40368

    • DOI

      10.1038/srep40368

    • NAID

      120005947171

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species2015

    • Author(s)
      Masaki Miya et al.
    • Journal Title

      Royal Society open science

      Volume: 2 Issue: 7 Pages: 150088-150088

    • DOI

      10.1098/rsos.150088

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Book] 実験医学, Vol.34, No.1, 103-107.2016

    • Author(s)
      岩崎渉、佐藤行人、源利文、山中裕樹、荒木仁志、宮正樹
    • Total Pages
      5
    • Publisher
      羊土社
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2018-03-22  

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