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Inferring the genomic structure of major cultured fishes by using high-density genetic map of tiger pufferfish

Research Project

Project/Area Number 18580175
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field General fisheries
Research InstitutionThe University of Tokyo

Principal Investigator

KIKUCHI Kiyoshi  The University of Tokyo, Graduate School of Agricultural and life sciences, Assistant Professor (20292790)

Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥3,890,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥390,000)
Fiscal Year 2007: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2006: ¥2,200,000 (Direct Cost: ¥2,200,000)
Keywordsgenome / linkage map / the tiger pufferfish / medaka / synteny / aquaculture / フグ / 比較ゲノム / 魚類 / 進化 / 育種 / ゲノム構造
Research Abstract

Recent advance in molecular genetics and genomics have enabled us to identify chromosomal regions underlying many agronomically important traits in domestic animals and crops. This genomic information can then be used for more effective selection than achieved by traditional methods. As genome sequences are powerful resource for the identification of loci, whole genome sequencing project for the major domestic animals and crops has been done. In contrast to the domestic animals and crops of which the number of species is relatively limited, the number of fish species important for aquaculture is more than dozen. Therefore, it would be still unpractical to generate draft sequence of all these fishes at the moment. An alternative way to understand, genomic structure of aquaculture fishes might be accomplished by precise inferring of the genome structure of "not yet sequenced genomes" by comparing genomes of model fishes such as fugu and medaka. Indeed, I previously predicted that the gen … More ome structure of fished belonging to Acanthopterygii should be well conserved by using genomic information from fugu and medaka. In this study I have done comprehensive comparison of the genome structure of model fishes, in order to infer the genome structure of major aquaculture fishes. The results are summarized as follows.
86% of the genome sequences of fugu were anchored to a high-density genetic map of fugu. This quality (coverage) of the map is ranked second among five model fishes (medaka, fugu, Tetraodon, zebrafish, stickleback).
By using the high-density map of fugu generated in this study, I inferred genome structure of the last common ancestor of fugu and Tetraodon. The result suggests that these fish experienced a few rearrangement events in genome since they diverged.
I comprehensively identified conserved genomic structure between fugu and medaka. Given the phylogenetic relationship of the major aquaculture fishes such as sea bream and yellowtail, the conserved genomic regions identified in this study should be also conserved among these fishes. Less

Report

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

    (39 results)

All 2008 2007 2006 Other

All Journal Article (16 results) (of which Peer Reviewed: 9 results) Presentation (22 results) Remarks (1 results)

  • [Journal Article] The sex-determining locus in the tiger pufferfish, Takifugu rubripes2007

    • Author(s)
      Kikuchi, K, Kai, et al.
    • Journal Title

      Genetics 175

      Pages: 2039-2042

    • 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] A teleost polymeric Ig receptor exhibiting two Ig-like domains transports tetrameric IgM into the skin2007

    • Author(s)
      Hamuro, K., Suetake, H, et al.
    • Journal Title

      J.Immunol. 178

      Pages: 5682-5689

    • 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] Description of a fugu CXC chemokine and two CXC receptor genes, and characterization of the effects of different stimulators on their expression2007

    • Author(s)
      Saha, N.R., Bei, J-X., et al.
    • Journal Title

      Fish Shellfish Immunol. 23

      Pages: 1324-1332

    • 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] Genomic organization and expression of CD8a and CD8b genes in fugu Takifugurubripes2007

    • Author(s)
      Suetake, H., Araki, K., et al.
    • Journal Title

      Fish Shellfish Immunol. 23

      Pages: 1107-1118

    • 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] The sex-determining locus in the tiger pufferfish, Takifugu rubripes2007

    • Author(s)
      Kikuchi, K, Kai, W., Hosokawa, et al.
    • Journal Title

      Genetics 175

      Pages: 2039-2042

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] A teleost polymeric Ig receptor exhibiting two Ig-like domains transports tetrameric IgM into the skin2007

    • Author(s)
      Hamuro, K., Suetake, H., et al.
    • Journal Title

      J.Immunol. 178

      Pages: 5682-5689

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Genomic organization and expression of CD8a and CD8b genes in fugu Takifugu rubripes2007

    • Author(s)
      Suetake, H., Araki, K., et al.
    • Journal Title

      Fish Shellfish Immunol. 23

      Pages: 1107-1118

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Two Interleukin(IL)-15 homologs from two distinct origins in fish2007

    • Author(s)
      Bei, J-X., Suetake, H., et al.
    • Journal Title

      Mol.Immunol. 43

      Pages: 860-869

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] The sex-determining locus in the tiger pufferfish, Takifugu rubripes2007

    • Author(s)
      Kikuchi, K, Kai, W., et al.
    • Journal Title

      Genetics 175

      Pages: 2039-2042

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of CD8 positive leukocytes in fugu (Takifugu rubripes) with antiserum against fugu CD8α2007

    • Author(s)
      Araki, K, Akatsu, K., et al.
    • Journal Title

      Dev. Comp. Immunol. 32

      Pages: 850-858

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A teleost polymeric Ig receptor exhibiting two Ig-like domains transports tetrameric IgM into the skin2007

    • Author(s)
      Hamuro, K., Suetake, H., et al.
    • Journal Title

      J. Immunol. 178

      Pages: 5682-5689

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Description of a fugu CXC chemokine and two CXC receptor genes, and characterization of the effects of different stimulators on their expression2007

    • Author(s)
      Saha, N. R., Bei, J-X, et al.
    • Journal Title

      Fish Shellfish Immunol. 23

      Pages: 1324-1332

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genomic organization and expression of CD8α and CD8β genes in fugu Takifugu rubripes2007

    • Author(s)
      Suetake, H., Araki, K., et al.
    • Journal Title

      Fish Shellfish Immunol 23

      Pages: 1107-1118

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The sex-determining locus in the tiger pufferfish, Takifugu rubripes2007

    • Author(s)
      Kikuchi, K, Kai, W., et al.
    • Journal Title

      Genetics (In press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A teleost polymeric Ig receptor exhibiting two Ig-like domains transports tetrameric IgM into the skin2007

    • Author(s)
      Hamuro K, Suetake H. et al.
    • Journal Title

      Journal of Immunology (In press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Two Interleukin (IL)-15 homologues in fish from two distinct origins2006

    • Author(s)
      Bei JX, Suetake H, et al.
    • Journal Title

      Molecular Immunology 43

      Pages: 860-869

    • Related Report
      2006 Annual Research Report
  • [Presentation] The sex-determining locus in fugu(the tiger pufferfish)2008

    • Author(s)
      Kikuchi, K.
    • Organizer
      The 54th international NIBB conference
    • Place of Presentation
      Aichi
    • Year and Date
      2008-02-27
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The sex-determining locus in fugu(the tiger pufferfish)2008

    • Author(s)
      菊池潔
    • Organizer
      The 54^<th> international NIBB conference
    • Place of Presentation
      Aichi
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The sex-determining locus in fugu (the tiger pufferfish)2008

    • Author(s)
      Kikuchi, K.
    • Organizer
      The 54^<th> international NIBB conference
    • Place of Presentation
      Aichi
    • Related Report
      2007 Annual Research Report
  • [Presentation] ゲノム配列情報は本当に水産に役立つのか?-フグゲノムの整備とその利用法2007

    • Author(s)
      菊池潔
    • Organizer
      第7回水産育種シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2007-11-26
    • 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] Is the genomic information of fishes really useful for fisheries?2007

    • Author(s)
      Kikuchi, K., et al.
    • Organizer
      The 7th Symposium on fish Genetics and Breeding Science
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-11-26
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] トラフグ性決定遺伝子座のマッピング2007

    • Author(s)
      甲斐渉・菊池潔, ら
    • Organizer
      日本動物遺伝育種学会第8回大会
    • Place of Presentation
      茨城
    • Year and Date
      2007-11-24
    • 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] Genetic mapping of fugu sex-determining locus2007

    • Author(s)
      Kia, W., Kikuchi, K, et al.
    • Organizer
      Annual meeting of JSABG
    • Place of Presentation
      Ibaraki
    • Year and Date
      2007-11-24
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] ゲノム育種によりトラフグの優良品種作出をめざす2007

    • Author(s)
      菊池潔・甲斐渉, ら
    • Organizer
      平成19年度日本水産学会大会中部支部大会
    • Place of Presentation
      福井
    • Year and Date
      2007-11-23
    • 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] Establishing new breeding technologies by using fugu genomic information2007

    • Author(s)
      Kikuchi, K., et al.
    • Organizer
      Midland meeting of JSFS
    • Place of Presentation
      Fukui
    • Year and Date
      2007-11-23
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] トラフグのヘルパーT細胞2007

    • Author(s)
      末武弘章・赤津可南子, ら
    • Organizer
      平成19年度日本魚病学会大会
    • Place of Presentation
      北海道
    • Year and Date
      2007-09-29
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Fugu helper T cell2007

    • Author(s)
      Suetake, H., Akatsu, K., et al.
    • Organizer
      Annual meeting of JSFP
    • Place of Presentation
      Hokkaido
    • Year and Date
      2007-09-29
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] トラフグIL-2の発現・機能解析2007

    • Author(s)
      三浦正晴・末武弘章, ら
    • Organizer
      日本比較免疫学会第19回学術集会
    • Place of Presentation
      静岡
    • Year and Date
      2007-08-21
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] トラフグB7ファミリー分子の同定2007

    • Author(s)
      菅又龍一・末武弘章, ら
    • Organizer
      日本比較免疫学会第19回学術集会
    • Place of Presentation
      静岡
    • Year and Date
      2007-08-21
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Expression and functional analysis of fugu IL-22007

    • Author(s)
      Miura, M, Suetake, H, et al.
    • Organizer
      The 19^<th> meeting of JSDC
    • Place of Presentation
      Shizuoka
    • Year and Date
      2007-08-21
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Identification of fugu B7 family2007

    • Author(s)
      Sugamata, R., Suetake, H., et al.
    • Organizer
      The 19^<th> meeting of JSDC
    • Place of Presentation
      Shizuoka
    • Year and Date
      2007-08-21
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A unique polymeric immunoglobulin receptor in teleost2007

    • Author(s)
      Suetake H, Hamuro K, et al.
    • Organizer
      13th International Congress of Mucosal Immunology
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-07-09
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The sex-determining locus in the tiger pufferfish(fugu)2007

    • Author(s)
      甲斐渉, 菊池潔 wt al.
    • Organizer
      第40回日本発生学会
    • Place of Presentation
      福岡
    • Year and Date
      2007-05-28
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Anterior-posterior patterning of a hypaxial muscle is controlled by Fgf signaling and Hox gene function2007

    • Author(s)
      Keina Matsumoto, Kiyoshi Kikuchi, et al.
    • Organizer
      第40回日本本発生学会
    • Place of Presentation
      福岡
    • Year and Date
      2007-05-28
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The sex-determining locus in the tiger pufferfish(fugu)2007

    • Author(s)
      Kai Wataru, Kiyoshi Kikuchi, et al.
    • Organizer
      Annual meeting of JSDB
    • Place of Presentation
      Fukuoka
    • Year and Date
      2007-05-28
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Anterior-posterior patterning of a hypaxial muscle is controlled by Fgf signaling and Hox gene function2007

    • Author(s)
      Keina Matsumoto, Kiyoshi Kikuchi, et al.
    • Organizer
      Annual meeting of JSDB
    • Place of Presentation
      Fukuoka
    • Year and Date
      2007-05-28
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A unique polymeric immunoglobulin receptor in teleost2007

    • Author(s)
      Suetake H, Hamuro K, et al.
    • Organizer
      13^<th> International Congress of Mucosal Immunology
    • Place of Presentation
      Tokyo
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The sex-determining locus in the tiger pufferfish (fugu)2007

    • Author(s)
      Kai, W., Kikuchi, K., et al
    • Organizer
      第40回日本発生学会
    • Place of Presentation
      福岡
    • Related Report
      2007 Annual Research Report
  • [Remarks]

    • URL

      http://www.se.a.u-tokyo.ac.jp/japanese.html

    • Related Report
      2007 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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