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2005 Fiscal Year Final Research Report Summary

Genome science towards the understanding of life

Research Project

Project/Area Number 12201001
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

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

Principal Investigator

KOHARA Yuji  National Institute of Genetics, Center for Genetic Resource Information, Professor, 生物遺伝資源情報総合センター, 教授 (70135292)

Co-Investigator(Kenkyū-buntansha) SUGANO Sumio  The University of Tokyo, Graduate School of Frontier Sciences, Professor, 大学院新領域創成科学研究科, 教授 (60162848)
OGASAWARA Naotake  Nara Institute of Science and Technology, Department of Bioinformatics and Genomics, Professor, バイオサイエンス研究科, 教授 (10110553)
TAKAGI Toshihisa  The University of Tokyo, Graduate School of Frontier Sciences, Professor, 大学院新領域創成科学研究科, 教授 (30110836)
GOJOBORI Takashi  National Institute of Genetics, Center for Information Biology and DDBJ, Profeser, 生命情報研究センター, 教授 (50162136)
YOSHIKAWA Hiroshi  JT Biohistory Reserch Hall, Advisor, 顧問 (70019876)
Project Period (FY) 2000 – 2005
KeywordsGenome Sequencing / EST / Resources / Outreach
Research Abstract

As the managing group of the 4 areas (this area and the other 3 genome areas), it performed the following activities;
1) Coordination among this 4 areas
2) Research resources; The DNA sequencing committee has performed genome sequencing of red algae (Cyanidioschyzon merolae), Ascidian (Ciona intestinalis), Y chromosome of liverwort (Marchantia polymorpha L), Medaka fish (Oryzias latipes) and wild mouse derived strain MSM by the whole genome shotgun strategy together with the end sequencing of fosmid and BAC clones. It also performed EST sequencing of nematode worms (Caenorhabditis elegans and Diploscapter sp.), Ascidian (Ciona intestinalis, Ciona savignyo and Halocynthia roretzi), Hagfish (Eptatretus burgeri), Medaka fish (Oryzias latipes), ciclid fish (Haplochromis chilotes), loach (Misgurnus anguillicaudatus), frog (Xenopus laevies), slime mold (Dictyostelium discodeum), red algae (Cyanidioschyzon merolae), moss (Physcomitrella patens subsp. patens), barley, wheat (Triticim aestivum cv. Chinese Spring), Japanese morning glory. The resource committee distributed the clones analyzed above to all over the world.
3) Outreach; The publicity committee provided information on the 4 areas to the public and research community. The social relationship committee held a social event named "Genome Square" altogether 8 times (in Tokyo, Kyoto and Fukuoka) during last 3 years, in which the research groups in the 4 areas presented their posters and research materials to communicate with the general public. The committee also discussed on the ethics issue in genome medicine.

  • Research Products

    (68 results)

All 2006 2005 2004 2003 2002 2001 Other

All Journal Article (66 results) Book (1 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.2006

    • Author(s)
      Eiichi Shoguchi, et al.
    • Journal Title

      Genome Research 16

      Pages: 297-303

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs) : paternally methylated DMRs contain less CpGs than maternally methylated DMRs.2006

    • Author(s)
      Kobayashi, H. et al.
    • Journal Title

      Cytogenet. Genome Res. 113

      Pages: 130-137

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] magp4 gene may contribute to the diversification of cichlid morphs and their speciation.2006

    • Author(s)
      Naoki Kobayashi, et al.
    • Journal Title

      Gene 373

      Pages: 126-133

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs) : paternally methylated DMRs contain less CpGs than maternally methylated DMRs.2006

    • Author(s)
      Kobayashi, et al.
    • Journal Title

      Cytogenet. Genome Res. 113 (Special Issue on Genomic Imprinting)

      Pages: 130-137

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes.2005

    • Author(s)
      Shimada M. et al.
    • Journal Title

      Cytogenetic and Genome Research 108(1-3)

      Pages: 83-90

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Identification of transcripts expressed preferentially in hemocytes of Ciona intestinalis that can be used as molecular markers.2005

    • Author(s)
      Wakoh, T. et al.
    • Journal Title

      DNA RESEARCH 11

      Pages: 345-352

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Hagfish Leukocytes Express a Paired Receptor Family with a Variable Domain Resembling Those of Antigen Receptors.2005

    • Author(s)
      Takashi Suzuki et al.
    • Journal Title

      J. Immunology 174

      Pages: 2885-2891

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The genome of the social amoeba Dictyostelium discoideum.2005

    • Author(s)
      L.Eichinger et al.
    • Journal Title

      Nature 435 No.7038

      Pages: 43-57

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Gimp1, A Novel Astacin Family Metalloproteinase Gene from East African Cichlids, Is Differentially Expressed Between Species During Growth.2005

    • Author(s)
      Teiya Kijimoto, et al.
    • Journal Title

      Mol. Biol. Evol. 22(8)

      Pages: 1649-1660

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes2005

    • Author(s)
      Shimada M et al.
    • Journal Title

      Cytogenetic and Genome Research 108(1-3)

      Pages: 83-90

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The genome of the social amoeba Dictyostelium discoideum.2005

    • Author(s)
      L.Eichinger
    • Journal Title

      Nature435 No7038

      Pages: 43-57

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] cimp1, A Novel Astacin Family Metalloproteinase Gene from East African Cichlids, Is Differentially Expressed Between Species During Growth.2005

    • Author(s)
      Teiya Kijimoto, et al.
    • Journal Title

      Mol. Biol. Evol. 22(8)

      Pages: 1649-1660

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.2004

    • Author(s)
      Motomichi Matsuzaki, et al.
    • Journal Title

      Nature 428

      Pages: 653-657

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae.2004

    • Author(s)
      Shinichiro Maruyama, et al.
    • Journal Title

      DNA RESEARCH 11

      Pages: 83-91

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Transcriptome analysis of hagfish leukocytes : a framework for understanding the immune system of jawless fishes.2004

    • Author(s)
      Takashi Suzuki, et al.
    • Journal Title

      Developmental & Comparative Immunology 28

      Pages: 993-1003

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Medaka genomics : a bridge between mutant phenotypes and gene function.2004

    • Author(s)
      Kiyoshi Naruse, et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 619-628

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.2004

    • Author(s)
      T.Kimura, et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 915-932

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Large-scale analysisi of the genes involved in fin regenerationand blastema formation in the medaka, Oryzias laptipes.2004

    • Author(s)
      Rei Katogi, et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 861-872

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum.2004

    • Author(s)
      Hideko Urushihara, et al.
    • Journal Title

      Nucl. Acids. Res. 32

      Pages: 1647-1653

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22.2004

    • Author(s)
      H.Watanabe, et al.
    • Journal Title

      Nature 429

      Pages: 382-388

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Extensive analysis of ORF sequences. from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock-Identity ofEST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller"-2004

    • Author(s)
      Masakatsu Watanabe, et al.
    • Journal Title

      Gene 343(2)

      Pages: 263-269

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Cyanobacterial genes transmitted to the nucleus before divergence of red algae in the chromista.2004

    • Author(s)
      Nozaki, H. et al.
    • Journal Title

      J. Mol. Evol. 59

      Pages: 103-113

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Comparative sequence analysis of a gene-dense region amongclosely related species of Drosophila melanogaster.2004

    • Author(s)
      Yoshihiro Kawahara et al.
    • Journal Title

      Genes & Genet. Systems 79,No.6

      Pages: 351-359

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.2004

    • Author(s)
      Motomichi Matsuzaki et al.
    • Journal Title

      Nature 428

      Pages: 653-657

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae.2004

    • Author(s)
      Shinichiro Maruyama et al.
    • Journal Title

      DNA RESEARCH 11

      Pages: 83-91

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Transcriptome analysis of hagfish leukocytes : a framework for understanding the immune system of jawless fishes.2004

    • Author(s)
      Takashi Suzuki et al.
    • Journal Title

      Developmental & Comparative Immunology 28

      Pages: 993-1003

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Medaka genomics : a bridge between mutant phenotypes and gene function.2004

    • Author(s)
      Kiyoshi Naruse et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 619-628

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.2004

    • Author(s)
      T.Kimura et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 915-932

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Large-scale analysisi of the genes involved in fin regenerationand blastema formation in the medaka, Oryzias laptipes.2004

    • Author(s)
      Rei Katogi et al.
    • Journal Title

      Mechanisms of Development 121

      Pages: 861-872

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum.2004

    • Author(s)
      Hideko Urushihara et al.
    • Journal Title

      Nucl. Acids. Res. 32

      Pages: 1647-1653

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22.2004

    • Author(s)
      H.Watanabe et al.
    • Journal Title

      Nature 429

      Pages: 382-388

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock-Identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller"-2004

    • Author(s)
      Masakatsu Watanabe et al.
    • Journal Title

      Gene 343(2)

      Pages: 263-269

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Cyanobacterial genes transmitted to the nucleus before divergence of red algae in the chromista.2004

    • Author(s)
      Nozaki, H et al..
    • Journal Title

      J. Mol. Evol. 59

      Pages: 103-113

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Comparative sequence analysis of a gene-dense region amongclosely related species of Drosophila melanogaster.2004

    • Author(s)
      Yoshihiro Kawahara et al.
    • Journal Title

      Genes & Genet. Systems79 No. 6

      Pages: 351-359

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Complete sequence and analysis of the plastid genome of theunicellular red alga Cyanidioschyzon merolae.2003

    • Author(s)
      Ohta, N, et al.
    • Journal Title

      DNA Research 10

      Pages: 67-77

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags.2003

    • Author(s)
      Ogihara, Y, et al.
    • Journal Title

      The Plant Journal 33

      Pages: 1001-1011

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Comparative genomics of the Physcomitrella gametophytic transcriptome and Arabidopsis genome : Implication for the land plant evolution.2003

    • Author(s)
      Tomoaki Nishiyama, et al.
    • Journal Title

      Proc. Natl. Acad. Sci. USA 100

      Pages: 8007-8012

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Construction of a gamete-enriched gene pool and RNAi-mediated functional analysis in Dictyostelium discoideum.2003

    • Author(s)
      Tetsuya Muramoto, et al.
    • Journal Title

      Mechanisms of Development 120

      Pages: 965-975

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalis I. Genes for bHLH transcription factors.2003

    • Author(s)
      Yutaka Satou, et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 213-221

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalisII. Genes for homeobox transcription factors.2003

    • Author(s)
      Shuichi Wada, et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 222-234

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalisIlI. Genes for Fox, ETS, nuclear receptors and NFB.2003

    • Author(s)
      Kasumi Yagi, et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 235-244

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Complete sequence and analysis of the plastid genome of theunicellular red alga Cyanidioschyzon merolae.2003

    • Author(s)
      Ohta, N et al.
    • Journal Title

      DNA Research 10

      Pages: 67-77

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags.2003

    • Author(s)
      Ogihara, Y et al.
    • Journal Title

      The Plant Journal 33

      Pages: 1001-1011

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Comparative genomics of the Physcomitrella gametophytic transcriptome and Arabidopsis genome : Implication for the land plant evolution.2003

    • Author(s)
      Tomoaki Nishiyama et al.
    • Journal Title

      Proc. Natl. Acad. Sci. USA 100

      Pages: 8007-8012

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Construction of a gamete-enriched gene pool and RNAi-mediated functional analysis in Dictyostelium discoideum.2003

    • Author(s)
      Tetsuya Muramoto et al.
    • Journal Title

      Mechanisms of Development 120

      Pages: 965-975

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalis I. Genes for bHLH transcription factors.2003

    • Author(s)
      Yutaka Satou et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 213-221

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalis II. Genes for homeobox transcription factors.2003

    • Author(s)
      Shuichi Wada et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 222-234

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A genomewide survey of developmentally relevant genes in Ciona intestinalis III. Genes for Fox, ETS, nuclear receptors and NFB.2003

    • Author(s)
      Kasumi Yagi et al.
    • Journal Title

      Development Genes and Evolution 213

      Pages: 235- 244

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Update of MAGEST : Maboya Gene Expression patterns and Sequence Tags.2002

    • Author(s)
      Takeshi Kawashima et al.
    • Journal Title

      Nucleic Acids Research 30・1

      Pages: 119-120

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] EST analysis of gene expression in testis of the ascidian Ciona intestinalis.2002

    • Author(s)
      Kazuo Inaba et al.
    • Journal Title

      Molecular Reproduction and Development Volume 62,Issue 4,

      Pages: 431-445

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Gene expression profiles in Ciona intestinalis cleavage-stage embryos.2002

    • Author(s)
      Shigeki Fujiwara, et al.
    • Journal Title

      Mechanisms of Development 112

      Pages: 115-127

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Gene expression profiles in young adult Ciona intestinalis2002

    • Author(s)
      Michio Ogasawara, et al.
    • Journal Title

      Dev. Genes Evol., 212

      Pages: 173-185

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Ciona intestinalis cDNA projects : expressed sequence tag analyses and gene expression profiles during embryogenesis.2002

    • Author(s)
      Yutaka Satou, et al.
    • Journal Title

      Gene 287

      Pages: 83-96

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Gene espression profiles in tadpole larvae of Ciona intestinalis.2002

    • Author(s)
      Takehiko Kusakabe, et al.
    • Journal Title

      Developmental Biology 242

      Pages: 188-203

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The draft genome of Ciona intestinalis : insights into chordateand vertebrate origins.2002

    • Author(s)
      Dehal P, Satou Y, et al.
    • Journal Title

      Science 298 Dec.l3issue

      Pages: 2157-2167

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] EST analysis of gene expression in testis of the ascidian Ciona intestinalis.2002

    • Author(s)
      Kazuo Inaba et al.
    • Journal Title

      Molecular Reproduction and Development Volume 62, Issue 4

      Pages: 431-445

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene expression profiles in Ciona intestinalis cleavage-stage embryos.2002

    • Author(s)
      Shigeki Fujiwara et al.
    • Journal Title

      Mechanisms of Development 112

      Pages: 115-127

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene expression profiles in young adult Ciona intestinalis2002

    • Author(s)
      Michio Ogasawara et al.
    • Journal Title

      Dev. Genes, Evol. 212

      Pages: 173-185

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Ciona intestinalis cDNA projects : expressed sequence tag analyses and gene expression profiles during embryogenesis.2002

    • Author(s)
      Yutaka Satou et al.
    • Journal Title

      Gene 287

      Pages: 83-96

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene espression profiles in tadpole larvae of Ciona intestinalis.2002

    • Author(s)
      Takehiko Kusakabe et al.
    • Journal Title

      Developmental Biology 242

      Pages: 188-203

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The draft genome of Ciona intestinalis : insights into chordateand vertebrate origins.2002

    • Author(s)
      Dehal P, et al.
    • Journal Title

      Science 298 Dec,13issue

      Pages: 2157-2167

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene expression profiles in Ciona intestinalis tailbud embryos.2001

    • Author(s)
      Satou, Y. et al.
    • Journal Title

      Development 128

      Pages: 2893-2904

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis.2001

    • Author(s)
      Nishikata, T. et al.
    • Journal Title

      Developmental Biology 238

      Pages: 315-331

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Gene expression profiles in Ciona intestinalis tailbud embryos.2001

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

      Development 128

      Pages: 2893-2904

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Transgenic analysis of medaka mesp-b enhancer in somitogenesis.

    • Author(s)
      Harumi Terasaki, et al.
    • Journal Title

      Development Growth and Differentiation (in press)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Transgenic analysis of medaka mesp-b enhancer in somitogenesis.

    • Author(s)
      Harumi Terasaki, et al.
    • Journal Title

      Development Growth and Differentiation (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Book] ゲノムサイエンスの新たなる挑戦(蛋白質核酸酵素増刊)2001

    • Author(s)
      榊佳之
    • Total Pages
      447
    • Publisher
      共立出版
    • Description
      「研究成果報告書概要(和文)」より
  • [Patent(Industrial Property Rights)] 植物の遺伝子に生じた特徴的な延期配列、及びそれを利用する方法2001

    • Inventor(s)
      佐藤和広, 武田和義, 小原雄治
    • Industrial Property Rights Holder
      国
    • Industrial Property Number
      特願 2001-387059、及び2001-387131
    • Filing Date
      2001-12-20
    • Description
      「研究成果報告書概要(和文)」より

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Published: 2008-05-27  

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