• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to project page

2009 Fiscal Year Final Research Report

Large-scale DNA sequencing and its application

Research Project

  • PDF
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
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
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.

  • Research Products

    (19 results)

All 2009 2008 2007 2006 Other

All Journal Article (17 results) Remarks (2 results)

  • [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)

      Pages: e6299

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

      Pages: D747-D752

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

  • [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

  • [Remarks] データベース/ソフトウェアNIG DNA Sequencing Center:

    • URL

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

  • [Remarks] マウスMSMゲノムDB

    • URL

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

URL: 

Published: 2011-06-18   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi