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Comparative Genomics Toward Understanding Genomic Bases of Evolution and Bio-Diversity

Research Project

Project/Area Number 16064101
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionNational Institute of Informatics

Principal Investigator

FUJIYAMA Asao  National Institute of Informatics, 情報学プリンシプル研究系, 教授 (60142311)

Co-Investigator(Kenkyū-buntansha) 佐藤 矩行  京都大学, 大学院・理学研究科, 教授 (30025481)
堀 寛  名古屋大学, 大学院・理学研究科, 教授 (60116663)
田畑 哲之  (財)かずさDNA研究所, 植物遺伝子研究部, 部長 (70197549)
矢田 哲士  京都大学, 大学院・情報学研究科, 准教授 (10322728)
小原 雄治  情報・システム研究機構国立遺伝学研究所, 遺伝資源研究センター, 教授 (70135292)
Project Period (FY) 2004 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥37,100,000 (Direct Cost: ¥37,100,000)
Fiscal Year 2009: ¥7,400,000 (Direct Cost: ¥7,400,000)
Fiscal Year 2008: ¥7,200,000 (Direct Cost: ¥7,200,000)
Fiscal Year 2007: ¥7,200,000 (Direct Cost: ¥7,200,000)
Fiscal Year 2006: ¥7,200,000 (Direct Cost: ¥7,200,000)
Fiscal Year 2005: ¥4,600,000 (Direct Cost: ¥4,600,000)
Fiscal Year 2004: ¥3,500,000 (Direct Cost: ¥3,500,000)
Keywordsゲノム / 比較ゲノム / ゲノム情報 / 染色体 / ゲノム科学 / 遺伝学
Research Abstract

The major objective of this project is to understand genomic bases of evolution and bio-diversity through genome analyses on various species that are important to those studies. We successfully analyzed genomes of amphioxus, chimpanzee and moss, for example, in addition to the development of software for comparative genomics. We also incorporated massively parallel genome analyzer to develop new field of genomics such as environmental genomics of symbiosis.

Report

(7 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • Research Products

    (38 results)

All 2009 2008 2007 2006 2005 2004 Other

All Journal Article (21 results) (of which Peer Reviewed: 6 results) Presentation (9 results) Book (4 results) Remarks (4 results)

  • [Journal Article] The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family2009

    • Author(s)
      Goto H, Watanabe K, Araragi N, Kageyama R, Tanaka K, Kuroki Y, Toyoda A, Hattori M, Sakaki Y, Fujiyama A, Fukumaki Y, Shibata H.
    • Journal Title

      BMC Evol Biol. 9

      Pages: 224-233

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family2009

    • Author(s)
      Goto H
    • Journal Title

      BMC Evol Biol. 9

      Pages: 224-233

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The amphioxus genome and the evolution of the chordate karyotype2008

    • Author(s)
      Putnam NH, et.al, including Y. Kuroki and A. Fujiyama
    • Journal Title

      Nature 453

      Pages: 1064-1071

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution2007

    • Author(s)
      Kasahara M, et. al. including Fujiyama and Kohara
    • Journal Title

      Nature 447

      Pages: 714-719

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Axial patterning in cephalochordates and the evolution of the organizer2007

    • Author(s)
      Yu, J.-K., Satou, Y., Holland, N.D., Shin-I, T., Kohara, Y., Satoh, N., Bronner-Fraser, M., and Holland, L.Z.
    • Journal Title

      Nature 445

      Pages: 613-617

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The genome size evolution of medaka(Oryzias latipes)and fugu(Takifugu rubripes).2007

    • Author(s)
      Imai S, Sasaki T, Shimizu A, Asakawa S, Hori H, Shimizu N
    • Journal Title

      Genes Genet. Syst. 82

      Pages: 135-144

    • NAID

      10024394027

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Axial patterning in cephalochordates and the evolution of the organizer2007

    • Author(s)
      Yu, J.-K
    • Journal Title

      Nature 445

      Pages: 613-617

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The DNA sequence of medaka chromosome LG22.2007

    • Author(s)
      Sasaki T
    • Journal Title

      Genomics 89

      Pages: 124-133

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Human chromosome 11 DNA sequence and analysis including novel gene identification2006

    • Author(s)
      Todd Taylor
    • Journal Title

      Nature 440

      Pages: 497-500

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis.2006

    • Author(s)
      著者 Kanamori, N.
    • Journal Title

      Proc. Natl. Acad. Sci U.S.A. 103

      Pages: 359-364

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway2006

    • Author(s)
      Kuroki, Y.
    • Journal Title

      NatureGenetics 38

      Pages: 158-167

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.2006

    • Author(s)
      Shoguchi, E.
    • Journal Title

      Genome Research 16

      Pages: 297-303

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Reversion mutation of ib oculocutaneous albinism to wild-type pigmentation in medaka fish2005

    • Author(s)
      Iida, A.
    • Journal Title

      Pigment Cell Res 18

      Pages: 382-384

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Sequencing the genespaces of Medicago truncatula and Lotus japonicus2005

    • Author(s)
      Young, N.D.
    • Journal Title

      Plant Physiol. 137

      Pages: 1174-1181

    • Related Report
      2005 Annual Research Report
  • [Journal Article] The C.elegans RUNX transcription factor MAB-2/RNT-1 is required for asymmetrical cell division of the T blast cell.2005

    • Author(s)
      Kagoshima, H.
    • Journal Title

      Developmental Biology 287

      Pages: 262-273

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 222004

    • Author(s)
      Watanabe, Hidemi
    • Journal Title

      Nature 429

      Pages: 382-388

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Genomic resources for ascidians : sequence/expression databases and genome projects2004

    • Author(s)
      Satoh, Noriyuki
    • Journal Title

      Methods in Cell Biol 74

      Pages: 759-774

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Low transposition frequency of the medaka fish Tol2 element may be due to extranuclear localization of its transposase2004

    • Author(s)
      Iida, Atsuo
    • Journal Title

      Genes Genet Systems 79

      Pages: 119-124

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Finishing the euchromatic sequence of the human genome2004

    • Author(s)
      International human Genome Sequencing Consortium
    • Journal Title

      Nature 431

      Pages: 931-945

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large scale sequencing of expressed sequence tags.2004

    • Author(s)
      Ogihara, Yasunari
    • Journal Title

      Genes Genet Syst. 79

      Pages: 227-232

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Hagfish Leukocytes Express a Paired Receptor Family with a Variable Domain Resembling Those of Antigen Receptors

    • Author(s)
      Suzuki, Takashi
    • Journal Title

      J Immunology (印刷中)

    • Related Report
      2004 Annual Research Report
  • [Presentation] 次世代シーケンサーによる個人ゲノム解読2009

    • Author(s)
      藤山秋佐夫
    • Organizer
      日本人類遺伝学会第54回大会
    • Place of Presentation
      グランドプリンスホテル高輪(東京都)
    • Year and Date
      2009-09-25
    • Related Report
      2009 Annual Research Report
  • [Presentation] 超大規模配列決定がもたらす生命研究へのインパクト2009

    • Author(s)
      藤山秋佐夫
    • Organizer
      日本分子生物物学会春期シンポジウム
    • Place of Presentation
      宮崎国際会議場、宮崎市)
    • Year and Date
      2009-05-12
    • Related Report
      2009 Final Research Report
  • [Presentation] Comprehensive analyses of Y chromosomes toward understanding of the male-specific genome functions2008

    • Author(s)
      Yoko Kuroki, Atsushi Toyoda, Shouji Tatsumoto, Yoshiyuki Sakaki and Asao Fujiyama
    • Organizer
      2008 Cold Spring Harbor Laboratory Meeting on the Biology of Genomes
    • Place of Presentation
      Cold Spring Harbor, USA
    • Related Report
      2008 Annual Research Report
  • [Presentation] Effect of hyper-parallel sequencers on comparative genomics2008

    • Author(s)
      Asao Fujiyama, Atsushi Toyoda, Yoko Kuroki, Tadasu Shin-I, Yuji Kohara
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Presentation] 緑藻クラミドモナスの完全長cDNA配列解析とゲ2008

    • Author(s)
      久保雄昭, 山野隆志, 佐竹知也, 鈴木穣, 菅野純夫, 藤山秋佐夫, 黒木陽子, 小原雄治, 新井理, 伊藤武彦, 福澤秀哉
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Presentation] 立襟鞭毛虫Monosiga ovataゲノムプロジェクト : II. 動物の初期進化における遺伝子多様化2008

    • Author(s)
      岩部直之, 隈啓一, 加藤和貴, 藤博幸, 廣瀬希, 佐々木剛, 菅裕, 宮田隆, 鈴木穣, 笠原雅弘, 新井理, 大石加寿子, 鹿児島浩, 豊田敦, 黒木陽子, 菅野純夫, 森下真一, 小原雄治, 藤山秋佐夫
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Presentation] 立襟鞭毛虫Monosiga ovataゲノムプロジェクト : I. ゲノム2008

    • Author(s)
      隈啓一, 岩部直之, 加藤和貴, 藤博幸, 廣瀬希, 菅裕, 宮田隆, 鈴木穣, 笠原雅弘, 新井理, 大石加寿子, 鹿児島浩, 豊田敦, 黒木陽子, 菅野純夫, 森下真一, 小原雄治, 藤山秋佐夫
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Presentation] オキゴンドウMHC領域のゲノム配列決定と比較ゲノム解析2008

    • Author(s)
      渡辺舞, 細道一善, 野口英樹, 黒木陽子, 豊田敦, 田中彰, 猪子英俊, 藤山秋佐夫, 椎名隆
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Presentation] Comparative analysis of glutamate receptor gene family between human and chimpanzee2008

    • Author(s)
      Hiroki Shibata, Hiroki Goto, Kazunori Watanabe, Yoko Kuroki, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki, Asao Fujiyama, Yasuyuki Fukumaki
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会(BMB2008)
    • Place of Presentation
      神戸(兵庫)
    • Related Report
      2008 Annual Research Report
  • [Book] ゲノムと遺伝子解析「医学のための細胞生物学、永田和弘、塩田浩平編」2009

    • Author(s)
      黒木陽子
    • Total Pages
      315
    • Publisher
      南山堂
    • Related Report
      2009 Annual Research Report
  • [Book] 細胞工学別冊(比較ゲノム学から読み解く生命システム、)監修 藤山秋佐夫2007

    • Author(s)
      藤山 秋佐夫
    • Total Pages
      196
    • Publisher
      秀潤社
    • Related Report
      2007 Annual Research Report
  • [Book] Handbook of Computational Molecular Biology2006

    • Author(s)
      Gotoh, O.
    • Publisher
      Chapman & Hall/CRC
    • Related Report
      2006 Annual Research Report
  • [Book] Handbook of Computational Molecular Biology2006

    • Author(s)
      Gotoh, O.
    • Total Pages
      36
    • Publisher
      Chapman & Hall/CRC
    • Related Report
      2005 Annual Research Report
  • [Remarks]

    • URL

      http://www.genome-sci.jp/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.genome-sci.jp/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://www.genome-sci.jp/

    • Related Report
      2008 Annual Research Report
  • [Remarks] 本班は、領域全体の調整と研究企画立案を任務とする総括班であり、実際の研究は行っていない。

    • Related Report
      2007 Annual Research Report

URL: 

Published: 2004-04-01   Modified: 2018-03-28  

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