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Simultaneous identification system for fisheries animals using ITS chip

Research Project

Project/Area Number 17380126
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Fisheries chemistry
Research InstitutionFisheries Research Agency

Principal Investigator

CHO Naritoshi  Fisheries Research Agency, National Researth Institute Fisheries Science, 研究室長 (70360766)

Co-Investigator(Kenkyū-buntansha) TAKEYAMA Haruko  Waseda University, 理工学術院, 教授 (60262234)
OOHATA Ichiro  National Researth Institute Fisheries Science, 中央水産研究所・水産遺伝子解析センター, 上席研究員 (40371843)
UENO Yasuhiro  Tohoku Regional Fisheries Research Institute, 東北区水産研究所・資源生態研究室, 研究室長 (50371810)
YOSHIMURA Taku  Seikai Regional Fisheries Researth Institute, 西海区水産研究所・沿岸資源研究室, 研究室長 (90371997)
Project Period (FY) 2005 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥7,140,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥540,000)
Fiscal Year 2007: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2006: ¥2,400,000 (Direct Cost: ¥2,400,000)
Fiscal Year 2005: ¥2,400,000 (Direct Cost: ¥2,400,000)
Keywordssimultaneous identification / multi-species / fisheries animlas / ITS region / DNA chip
Research Abstract

Sample size collected from wide variety of marine animals reached to 1,000 species at the end of 2007. Among them, we attempted to amplify the homologous. ITS1 region in 775 individuals from 600 species and observed successful single fragment amplification in 688 individuals. We determined entire or partial nucleotide sequences of 315 individuals from 273 species. All these sequences determined have been deposited to the database. We investigated the length and GC content of the ITS1 region that may have significant correlation with hybridization efficiency. No species was found to have ITS1shorter than 100 bp. In general, ITS1 of vertebrate(fishes) was GC richer(56.8 to 78 %) and longer(318 to 2300 bp) than invertebrates. Specifically, gelatinous animal(Cnidana and Ctenophora) were observed to have shorter ITS1(118 to 422 bp) with lower GC content(35.8 to 61.7 %) than the other animal taxa. Mollusca and Crustacea were diverse group in ITSl size, ranging from 108 to 1118 bp for the former and from 182 to 1613 bp for the later. No apparent relationship between the length and GC content was observed. The prototype chip designed last year was spotted with PCR products, and we could not get better discrimination results. In this year, we designed oligo probes(c. a. 60 nt) from 200 species, which do not share any similar nucleotide sequences one another, and these probes were spotted on the chip. Hybridization experiment using PCR products with this chip indicated the efficiency for species-specific hybridization was considerably improved.

Report

(4 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (32 results)

All 2008 2007 2006 Other

All Journal Article (24 results) (of which Peer Reviewed: 10 results) Presentation (5 results) Book (3 results)

  • [Journal Article] Preliminary observation on length and GC content variation in the ribosomal first internal transcribed spacer(ITS1) of marine animals.2008

    • Author(s)
      Chow, S., Ueno, Y., Toyokawa, M., Oohara, I. and Takeyama, H
    • Journal Title

      Marine Biotechnology (in print)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Efficient analysis for natural diet of marine animal larvae using peptide nucleic acid(PNA)-mediated PCR clamping.2008

    • Author(s)
      Takeyama, H., Suzuki, S., Yokouchi, T., Matsunaga, T. and Chow, S.
    • Journal Title

      Marine Biotechnology (in print)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Molecular evidence for synonymy of the genera Moroteuthis and Onykia and identification of their paralarvae from northern Hawaiian waters.2007

    • Author(s)
      Wakabayashi, T., Kubodera, T., Sakai, M., Ichii, T.and Chow, S.
    • Journal Title

      J.Mar.Biol.Ass.U.K. 87

      Pages: 959-965

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Boundary between the north and south Atlantic populations of the swordfish(Xiphias gladius)inferred by a single nucleotide polymorphism at calmodulin gene intron.2007

    • Author(s)
      Chow, S., Clarke, S., Nakadate, M.and Okazaki, M.
    • Journal Title

      Marine Biology 152

      Pages: 87-93

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] High-throughput SNP detection using nano-scale engineered biomagnetite.2007

    • Author(s)
      Matsunaga, T., Maruyama, K., Takeyama, H., Katoh, T.
    • Journal Title

      Biosens.Bioelectron. 22

      Pages: 2315-2321

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Fully automated immunoassay for detection of prostate-specific antigen using nano-magnetic beads and micro-polystyrene bead composites,'Beads on Beads'.2007

    • Author(s)
      Matsunaga, T., Maeda, Y., Yoshino, T., Takeyama, H., Takahashi, M., Ginya, H., Asahina, J.and Tajima, H.
    • Journal Title

      Anal.Chim.Acta 597

      Pages: 331-339

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Molecular evidence for synonymy of the genera Moroteuthis and Onykia and identification of their paralarvae from northern Hawaiian waters.2007

    • Author(s)
      Wakabayashi, T., Kubodera, T., Sakai, M., Ichii, T. and Chow, S.
    • Journal Title

      J. Mar. Biol. Ass. U.K. 87

      Pages: 959-965

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Boundary between the north and south Atlantic populations of the swordfish(Xiphias gladius) inferred by a single nucleotide polymorphism at calmodulin gene intron.2007

    • Author(s)
      Chow, S., Clarke, S., Nakadate, M. and Okazaki, M.
    • Journal Title

      Marine Biology 152

      Pages: 87-93

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] High-throughput SNP detection using nano-scale engineered biomagnetite.2007

    • Author(s)
      Matsunaga, T., Maruyama, K., Takeyama, H., Katoh, T.
    • Journal Title

      Biosens. Bioelectron. 22

      Pages: 2315-2321

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Fully automated immunoassay for detection of prostate-specific antigen using nano-magnetic beads and micro-polystyrene bead composites, Beads on Beads.2007

    • Author(s)
      Matsunaga, T., Maeda, Y., Yoshino, T., Takeyama, H., Takahashi, M., Ginya, H., Asahina, J. and Tajima, H
    • Journal Title

      Anal. Chim. Acta 597

      Pages: 331-339

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] All about tuna 「Phylogenetic relationships among tuna species inferred from DNA analysis」2007

    • Author(s)
      Chow, S.
    • Journal Title

      Illustrated Book for Fisheries Products, Supplement 1

      Pages: 26-28

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] All about tuna 「Species identification using DNA for morphologically similar species」2007

    • Author(s)
      Chow, S.
    • Journal Title

      Illustrated Book for Fisheries Products, Supplement 1

      Pages: 145-145

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Molecular evidence for synonymy of the genera Moroteuthis and Onykia and identification of their paralarvae from northern Hawaiian waters.2007

    • Author(s)
      Wakabayashi, T., Kubodera, T., Sakai, M., Ichii, T. and Chow, S.
    • Journal Title

      Journal of Marine Biological Association U.K. 87

      Pages: 959-965

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Boundary between the north and south Atlantic populations of the sword fish(Xiphias gladius) inferred by a single nucleotide polymorphism at calmodulin gene intron.2007

    • Author(s)
      Chow, S., Clarke, S., Nakadate, M. and Okazaki, M.
    • Journal Title

      Marine Biology 152

      Pages: 87-93

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-throughput SNP detection using nano-scale engineered biomagnetite.2007

    • Author(s)
      Matsunaga, T., Maruyama, K., Takeyama, H. and Katoh, T.
    • Journal Title

      Biosensors and Bioelectronics 22

      Pages: 2315-2321

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fully automated immunoassay for detection of prostate-specific antigen using nano-magnetic beads and micro-polystyrene bead composites, 'Beads on Beads'.2007

    • Author(s)
      Matsunaga, T., Maeda, Y., Yoshino, T., Takeyama, H., Takahashi, M., Ginya, H., Asahina, J. and Tajima, H.
    • Journal Title

      Analytica Chimica Acta 597

      Pages: 331-339

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Eukaryotes from the hepatopancreas of lobster phyllosoma larvae.2007

    • Author(s)
      Suzuki, N., Murakami, K., Takeyama, H., Chow, S.
    • Journal Title

      Bulletin of Fisheries Research Agency 20

      Pages: 1-7

    • NAID

      40015433285

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Discrimination of DNA mismatches by direct force measurement for identification of tuna species.2006

    • Author(s)
      Tanaka, T., Sasaki, T., Amemiya, Y., Takeyama, H., Chow, S., Matsunaga, T.
    • Journal Title

      Analytica Chimica Acta 561

      Pages: 150-155

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A late stage phyllosoma larva of the spiny lobster Panulirus echinatus Smith, 1869 (Crustacea : Palinuridae) identified by DNA analysis.2006

    • Author(s)
      Konishi, K., Suzuki, N., Chow, S.
    • Journal Title

      Journal of Plankton Research 28

      Pages: 841-845

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Identification of mid to final stage phyllosoma larvae of the genus Panulirus White, 1847 collected in the Ryukyu Archipelago.2006

    • Author(s)
      Chow, S., Yamada, H., Suzuki, N.
    • Journal Title

      Crustaceana 79

      Pages: 745-764

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Molecular species identification of spiny lobster phyllosoma larvae of the genus Panulirus from the northwestern Pacific.2006

    • Author(s)
      Chow, S., Suzuki, N., Imai, H., Yoshimura, T.
    • Journal Title

      Marine Biotechnology 8

      Pages: 260-267

    • NAID

      10018003021

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Phylogenetic relationships among Thunnus tuna species inferred from rDNA ITS1 sequence.2006

    • Author(s)
      Chow, S., Nakagawa, T., Suzuki, N., Takeyama, H., Matsunaga, T.
    • Journal Title

      Journal of Fish Biology 68

      Pages: 24-35

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Preliminary observation on length and GC content variation in the ribosomal first internal transcribed spacer(ITS1)of marine animals.

    • Author(s)
      Chow, S., Ueno, Y., Toyokawa, M., Oohara, I.and Takeyama, H
    • Journal Title

      Marine Biotechnology (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Efficient analysis for natural diet of marine animal larvae using peptide nucleic acid(PNA)-mediated PCR clamping.

    • Author(s)
      Takeyama, H., Suzuki, S., Yokouchi, T., Matsunaga, T.and Chow, S.
    • Journal Title

      Marine Biotechnology (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Presentation] マルチプレックスPCRを用いたメバチ産地判別迅速化の試み.2008

    • Author(s)
      野原健司・仙波靖子・鈴木伸明・張 成年・岡本浩明
    • Organizer
      平成20年度日本水産学会春季大会
    • Place of Presentation
      静岡
    • Year and Date
      2008-03-30
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] An attempt to identify origin of bigeye tuna Thunnus obesus using multi-plex PCR.2008

    • Author(s)
      Nohara, K., Senba, Y., Suzuki, N., Chow, S. and Okamoto, H.
    • Organizer
      The Japanese Society of Fisheries Science
    • Year and Date
      2008-03-30
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] マルチプレックスPCRを用いたメバチ産地判別迅速化の試み2008

    • Author(s)
      野原健司・仙波靖子・鈴木伸明・張成年・岡本浩明
    • Organizer
      平成20年度日本水産学会春季大会
    • Place of Presentation
      静岡
    • Year and Date
      2008-03-30
    • Related Report
      2007 Annual Research Report
  • [Presentation] RFLP/SSCP法を用いたクロマグロThunnus orientalisのmtDNA多様性解析2007

    • Author(s)
      鈴木伸明・升間主計・田邉智唯・青沼佳方・張 成年
    • Organizer
      平成19年度日本水産学会秋季大会
    • Place of Presentation
      函館
    • Year and Date
      2007-09-27
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] mtDNA diversity evaluation in the northern bluefin tuna Thunnus orientaris using RFLP/SSCP.2007

    • Author(s)
      Suzuki, N., Masuma, S., Tanabe, T., Aonuma, Y. and Chow, S.
    • Organizer
      The Japanese Society of Fisheries Science
    • Year and Date
      2007-09-27
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Book] 食材魚貝大図鑑 別巻1 まぐろの全て 「マグロの類縁関係-DNAに基づく分析から」2007

    • Author(s)
      張 成年
    • Total Pages
      3
    • Publisher
      平凡社
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Book] 食材魚貝大図鑑 別巻1 まぐろの全て 「DNAを使った種判別-外見でわからないものを判定する」2007

    • Author(s)
      張 成年
    • Total Pages
      1
    • Publisher
      平凡社
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Book] 食材魚貝大図鑑 別巻 マグロのすべて2007

    • Author(s)
      張 成年
    • Total Pages
      3
    • Publisher
      平凡社
    • Related Report
      2007 Annual Research Report

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Published: 2005-04-01   Modified: 2016-04-21  

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