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2007 Fiscal Year Final Research Report Summary

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
Keywordsgenome / linkage map / the tiger pufferfish / medaka / synteny / aquaculture
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

  • Research Products

    (28 results)

All 2008 2007

All Journal Article (8 results) (of which Peer Reviewed: 4 results) Presentation (20 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
    • 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
    • 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
    • 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
    • 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
  • [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
  • [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
  • [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
  • [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
    • Year and Date
      20080227-20080229
    • Description
      「研究成果報告書概要(和文)」より
  • [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
  • [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
    • Year and Date
      20070709-20070712
    • Description
      「研究成果報告書概要(和文)」より
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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

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Published: 2011-06-18  

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