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Large-scale DNA sequencing and its application

Research Project

Project/Area Number 17020008
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, 所長 (70135292)

Project Period (FY) 2005 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥889,000,000 (Direct Cost: ¥889,000,000)
Fiscal Year 2009: ¥179,100,000 (Direct Cost: ¥179,100,000)
Fiscal Year 2008: ¥177,500,000 (Direct Cost: ¥177,500,000)
Fiscal Year 2007: ¥177,500,000 (Direct Cost: ¥177,500,000)
Fiscal Year 2006: ¥177,400,000 (Direct Cost: ¥177,400,000)
Fiscal Year 2005: ¥177,500,000 (Direct Cost: ¥177,500,000)
Keywordsゲノム / cDNAライブラリー / 全ゲノムショットガン / EST / DNAシーケンサー / アッセンブラ / WGS(全ゲノムショットガン) / ゲノムシーケンシング / フォスミド / SNP / 比較ゲノム / SAGE / whole genome shotgun sequencing
Research Abstract

We established a large-scale (Sanger) DNA sequencing system through the review, improvement and cost reduction of the sequencing process step by step, leading to allow us to obtain 6 million (Sanger) reads per year. Based on the requests from the researchers in the grant group, we produced 3.4 million EST reads for 92 cDNA libraries from 16 organisms. We also produced 19.4 million reads for whole genome shotgun sequencing of 7 organisms including wild-derived mouse, a hemichordata, water bears, the choanoflagellate Monosiga ovata. Altogether 24 million reads were produced during the project period. To analyze the reads more closely, we developed a work-bench for genome finishing and a viewer for polymorphism identification. For the next generation DNA sequencing system, we set up a computer system with a security system that is essential for personal genomics and performed various DNA sequencing. Furthermore, we developed a viewer system for polymorphism identification and a system for cDNA full sequencing. Solexa multiplexing data analysis was also tested.

Report

(6 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
  • Research Products

    (47 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (40 results) (of which Peer Reviewed: 15 results) Presentation (5 results) Remarks (2 results)

  • [Journal Article] Large-scale analysis of full-length cDNAs from the tomato(Solanum lycopersicum)cultivar Micro-Tom, a reference system for the Solanaceae genomics2010

    • Author(s)
      Koh Aoki
    • Journal Title

      BMC Genomics 11(1)

      Pages: 210-210

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Polycystic Kidney Disease in the Medaka (Oryzias latipes) pc Mutant Caused by a Mutation in the Gli-Similar3 (glis3) Gene.2009

    • Author(s)
      Hashimoto, H., Miyamoto, R., Watanabe, N., Shiba, D., Ozato, K., Inoue, C., Kubo, Y., Koga, A., Jindo, T., Narita, T., Naruse, K., Ohishi, K., Nogata, K., Shin-I, T., Asakawa, S., Shimizu, N., Miyamoto, T., Mochizuki, T., Yokoyama, T., Hori, H., Takeda, H., Kohara, Y., Wakamatsu
    • Journal Title

      PLoS ONE 4(7)

    • Related Report
      2009 Final Research Report
  • [Journal Article] Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources.2009

    • Author(s)
      K. Sato, T. Shin-i, M. Seki, K. Shinozaki, H. Yoshida, K. Takeda, Y. Yamazaki, M. Conte,, Y. Kohara
    • Journal Title

      DNA RESEARCH 16

      Pages: 81-89

    • NAID

      120005398236

    • Related Report
      2009 Final Research Report
  • [Journal Article] Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets.2009

    • Author(s)
      N. Kobayashi, M. Watanabe, T. Horiike, Y. Kohara, N. Okada
    • Journal Title

      Gene 441

      Pages: 187-191

    • Related Report
      2009 Final Research Report
  • [Journal Article] Chromatinassociated periodicity in genetic variation downstream of transcriptional start sites2009

    • Author(s)
      S. Sasaki, C.C. Mello, A. Shimada, Y. Nakatani, S. Hashimoto, M. Ogawa, K. Matsushima, S.G. Gu, M. Kasahara, B. Ahsan, A. Sasaki, T. Saito, Y. Suzuki, S. Sugano, Y. Kohara, H. Takeda, A. Fire, S. Morishita
    • Journal Title

      Science 323

      Pages: 401-404

    • Related Report
      2009 Final Research Report
  • [Journal Article] Polycystic Kidney Disease in the Medaka(Oryzias latipes)pc Mutant Caused by a Mutation in the Gli-Similar3(glis3)2009

    • Author(s)
      Hisashi Hashimoto
    • Journal Title

      Gene.PLoS ONE 4(7)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites2009

    • Author(s)
      Shin Sasaki
    • Journal Title

      Science 323

      Pages: 401-404

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of 5006 Full-Length CDNAs in Barley : A Tool for Accessing Cereal Genomics Resources2009

    • Author(s)
      Kazuhiro SATO
    • Journal Title

      DNA RESEARCH 16

      Pages: 81-89

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The International Silkworm Genome Consortium: The genome of a lepidopteran model insect, the silkworm Bombyx mori.2008

    • Journal Title

      Insect Biochem. & Mol. Biol 38

      Pages: 1036-1045

    • Related Report
      2009 Final Research Report
  • [Journal Article] A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae2008

    • Author(s)
      J-K. Yu, M-C. Wang, T. Shin-I, Y. Kohara, L.Z. Holl,, N. Satoh, Y. Satou
    • Journal Title

      Development Genes, Evolution 218

      Pages: 723-727

    • Related Report
      2009 Final Research Report
  • [Journal Article] The amphioxus genome, the evolution of chordate karyotype2008

    • Author(s)
      N. H. Putnam, T. Butts, D. E. K. Ferrier, R. F. Furlong, U. Hellsten, T. Kawashima, M. Robinson-Rechavi, E. Shoguchi, A. Terry, Jr-K. Yu, E. Benito-Gutierrez, I. Dubchak, J. Garcia-Fernandez, I. V. Grigoriev, A. C. Horton, P. J. de Jong, J. Jurka, V. Kapitonov, Y. Kohara, Y. Kuroki, E. Lindquist, S. Lucas, K. Osoegawa, L. A. Pennacchio, A.A. Salamov, Y. Satou, T. Sauka-Spengler, J. Schmutz, T. Shin-I, A. Toyoda, J. J. Gibson-Brown, M. Bronner-Fraser, A. Fujiyama, L. Z. Holland, P. W. H. Holland, N. Satoh, D. S. Rokhsar
    • Journal Title

      Nature 453

      Pages: 1064-1071

    • Related Report
      2009 Final Research Report
  • [Journal Article] Bombyx small RNAs: Genomic defense system against transposons in the silkworm, Bombyx mori2008

    • Author(s)
      S. Kawaoka, N. Hayashi, S. Katsuma, H. Kishino, Y. Kohara, K. Mita,, T. Shimada
    • Journal Title

      Insect Biochemistry, Molecular Biology 38

      Pages: 1058-1065

    • Related Report
      2009 Final Research Report
  • [Journal Article] The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of L, by Plants2008

    • Author(s)
      S. A. Rensing, D. Lang, A. D. Zimmer, A. Terry, A. Salamov, H. Shapiro, T. Nishiyama, P-F. Perroud, E. A. Lindquist, Y. Kamisugi, T. Tanahashi, K. Sakakibara, T. Fujita, K. Oishi, T. Shin-I, Y. Kuroki, A. Toyoda, Y. Suzuki, S. Hashimoto, K. Yamaguchi, S. Sugano, Y. Kohara, A. Fujiyama, A. Anterola, S. Aoki, N. Ashton, W. B. Barbazuk, E. Barker, J. L. Bennetzen, R. Blankenship, S. H. Cho, S. K. Dutcher, M. Estelle, J. A. Fawcett, H. Gundlach, K. Hanada, A. Heyl, K. A. Hicks, J. Hughes, M. Lohr, K. Mayer, A. Melkozernov, T. Murata, D. R. Nelson, B. Pils, M. Prigge, B. Reiss, T. Renner, S. Rombauts, P. J. Rushton, A. Sanderfoot, G. Schween, S-H. Shiu, K. Stueber, F. L. Theodoulou, H. Tu, Y. Van de Peer, P. J. Verrier, E. Waters, A. Wood, L. Yang, D. Cove, A. C. Cuming, M. Hasebe, S. Lucas, B. D. Mishler, R. Reski, I. V. Grigoriev, R. S. Quatrano, J. L. Boore
    • Journal Title

      Science 319

      Pages: 64-69

    • Related Report
      2009 Final Research Report
  • [Journal Article] UTGB/medaka: genomic resource database for medaka biology.2008

    • Author(s)
      B. Ahsan, D. Kobayashi, T. Yamada, M. Kasahara, S. Sasaki, T. L. Saito, Y. Nagayasu, K. Doi, Y. Nakatani, W. Qu, T. Jindo, A. Shimada, K. Naruse, A. Toyoda, Y. Kuroki, A. Fujiyama, T. Sasaki, A. Shimizu, S. Asakawa, N. Shimizu, S. Hashimoto, J. Yang, Y. Lee, K. Matsushima, S. Sugano, M. Sakaizumi, T. Narita, K. Ohishi, S. Haga, F. Ohta, H. Nomoto, K. Nogata, T. Morishita, T. Endo, T. Shin-I, H. Takeda, Y. Kohara, S. Morishita
    • Journal Title

      Nucleic Acids Research 36

    • Related Report
      2009 Final Research Report
  • [Journal Article] Genomic defense system against transposons in the silkworm, Bombyxmori2008

    • Author(s)
      Shinpei Kawaoka
    • Journal Title

      Insect Biochemistry and Molecular Biology (Special Issue on Bombyx Genome) 38

      Pages: 1058-1065

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The amphioxus genome and the evolution of chordate karyotype2008

    • Author(s)
      Nicholas H. Putnam
    • Journal Title

      Nature 453

      Pages: 1064-1071

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A cDNA resource for the cephalochordate amphioxus Branchiostoma flor idea2008

    • Author(s)
      Jr-Kai Yu
    • Journal Title

      Development Genes and Evolution 218

      Pages: 723-727

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The genome of a lepidopteran model insect, the silkworm Bombyx mori2008

    • Author(s)
      The International Silkworm Genome Consortium
    • Journal Title

      Insect Biochemistry and Molecular Biology 38

      Pages: 1036-1045

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Retrotransposon Silencing by DNA Methylation can Drive Mammalian Genomic Imprinting.2008

    • Author(s)
      Stefan A. Rensing
    • Journal Title

      Science 319

      Pages: 64-69

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates.2007

    • Author(s)
      Y. Nakatani, H. Takeda, Y. Kohara, S. Morishita
    • Journal Title

      Genome Research 17(9)

      Pages: 1254-65

    • Related Report
      2009 Final Research Report
  • [Journal Article] Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis.2007

    • Author(s)
      F. Gyoja, Y. Satou, T. Shin-i, Y. Kohara, B.J. Swalla, N. Satoh
    • Journal Title

      Developmental Biology 307

      Pages: 460-482

    • Related Report
      2009 Final Research Report
  • [Journal Article] The medaka draft genome, new insights into vertebrate genome evolution.2007

    • Author(s)
      M. Kasahara, K. Naruse, S. Sasaki, Y. Nakatani, W. Qu, B. Ahsan, T. Yamada, Y. Nagayasu, K. Doi, Y. Kasai, T. Jindo, D. Kobayashi, A. Shimada, A. Toyoda, Y. Kuroki, A. Fujiyama, T. Sasaki, A. Shimizu, S. Asakawa, N. Shimizu, S. Hashimoto, J. Yang, Y. Lee, K. Matsushima, S. Sugano, M. Sakaizumi, T. Narita, K. Ohishi, S. Haga, F. Ohta, H. Nomoto, K. Nogata, T. Morishita, T. Endo, T. Shin-I, H. Takeda, S. Morishita, Y. Kohara
    • Journal Title

      Nature 446

      Pages: 714-719

    • Related Report
      2009 Final Research Report
  • [Journal Article] Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system.2007

    • Author(s)
      K. T. Yamato, K. Ishizaki, M. Fujisawa, S. Okada , S. Nakayama, M. Fujishita, H. Bando, K. Yodoya, K. Hayashi, T. Bando, A. Hasumi, T. Nishio, R. Sakata, M. Yamamoto, A. Yamaki, M. Kajikawa, T. Yamano, T. Nishide, S-H. Choi, Y. Shimizu-Ueda, T. Hanajiri, M. Sakaida, K. Kono, M. Takenaka, S. Yamaoka, C. Kuriyama, Y. Kohzu, H. Nishida, A. Brennicke, T. Shin-i, Y. Kohara, T. Kohchi, H. Fukuzawa, K. Ohyama
    • Journal Title

      PNAS 104

      Pages: 6472-6477

    • Related Report
      2009 Final Research Report
  • [Journal Article] Axial patterning in cephalochordates, the evolution of the organizer.2007

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

      Nature 445

      Pages: 613-617

    • Related Report
      2009 Final Research Report
  • [Journal Article] Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system.2007

    • Author(s)
      Katsuyuki T.
    • Journal Title

      Proceedings of National Academy of Science, USA 104

      Pages: 6472-6477

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The medaka draft genome and new insights into vertebrate genome evolution.2007

    • Author(s)
      Masahiro Kasahara.
    • Journal Title

      Nature 446

      Pages: 714-719

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Retrotransposon Silencing by DNA Methylation can Drive Mammalian Genomic Imprinting.2007

    • Author(s)
      Shunsuke Suzuki
    • Journal Title

      PLos Genetics 3, No.4

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of large scale expression sequenced tags(ESTs)from the anural ascidian, Molgula tectiformis.2007

    • Author(s)
      Fuki Gyoja
    • Journal Title

      Developmental Biology 307

      Pages: 460-482

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates.2007

    • Author(s)
      Yoichiro Nakatani
    • Journal Title

      Genome Research 17(9)

      Pages: 1254-65

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

    • Author(s)
      Jr-Kai Yu
    • Journal Title

      Nature 445

      Pages: 613-617

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system.2007

    • Author(s)
      Katsuyuki T. Yamato
    • Journal Title

      PNAS 104

      Pages: 6472-6477

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Retrotransposon Silencing by DNA Methylation can Drive Mammalian Genomic Imprinting2007

    • Author(s)
      Shunsuke Suzuki
    • Journal Title

      PLos Genetics 3

    • Related Report
      2006 Annual Research Report
  • [Journal Article] magp4 gene may contribute to the diversification of cichlid morphs, their speciation.2006

    • Author(s)
      N. Kobayashi, M. Watanabe, T. Kijimoto, K. Fujimura, M. Nakazawa, K. Ikeo, Y. Kohara, T. Gojobori, N. Okada
    • Journal Title

      Gene 373

      Pages: 126-133

    • Related Report
      2009 Final Research Report
  • [Journal Article] Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis2006

    • Author(s)
      E. Shoguchi, T. Kawashima, Y. Satou, M. Hamaguchi, T. Sin-I, Y. Kohara, N. Putnam, D.S. Rokhsar, N. Satoh
    • Journal Title

      Genome Research 16

      Pages: 297-303

    • Related Report
      2009 Final Research Report
  • [Journal Article] Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.2006

    • Author(s)
      Eiichi Shoguchi
    • Journal Title

      Genome Research 16

      Pages: 297-303

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Bisulfate sequencing an 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
    • Journal Title

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

      Pages: 130-137

    • Related Report
      2005 Annual Research Report
  • [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
    • Journal Title

      Mol.Biol.Evol. 22(8)

      Pages: 1649-1660

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets

    • Author(s)
      Naoki Kobayashi
    • Journal Title

      Gene (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of large scale expression sequenced tags (ESTs) from the anuraI ascidian, Molgula tectiformis.

    • Author(s)
      Fuki Gyoja
    • Journal Title

      Developmental Biology (in press)2007

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Transgenic analysis of medaka mesp-b enhancer in somitogenesis.

    • Author(s)
      Harumi Terasaki
    • Journal Title

      Development Growth and Differentiation (in press)

    • Related Report
      2005 Annual Research Report
  • [Presentation] 非分化性の社会性アメーバ、Acytostelium の遺伝子解析2010

    • Author(s)
      漆原秀子
    • Organizer
      第4回日本ゲノム微生物学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2010-03-07
    • Related Report
      2009 Annual Research Report
  • [Presentation] ChlamyBase, Chlamydomonas genome database based on the genomic resources of matingtype minus strain and transcriptome data obtained by massively paralleled sequencing2009

    • Author(s)
      Takeaki Kubo
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] Comparative analysis of the Y chromosomes to understand the male-specifi c character in mammalian genome evolution2009

    • Author(s)
      Yoko Kuroki
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] Construction of the genome database and draft genome sequence analysis of anhydrobiotic extremotolerant tardigrade2009

    • Author(s)
      Toshiaki Katayama
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] 極限環境耐性動物クマムシのゲノム解析と機能プロテオミクス2009

    • Author(s)
      國枝武和
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-10
    • Related Report
      2009 Annual Research Report
  • [Remarks] データベース/ソフトウェアNIG DNA Sequencing Center:

    • URL

      http://dolphin.lab.nig.ac.jp/

    • Related Report
      2009 Final Research Report
  • [Remarks] マウスMSMゲノムDB

    • URL

      http://molossinus.lab.nig.ac.jp/msmdb/index.jsp

    • Related Report
      2009 Final Research Report

URL: 

Published: 2005-04-01   Modified: 2018-03-28  

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