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Construction of medaka BAC library

Research Project

Project/Area Number 11236209
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKeio University

Principal Investigator

ASAKAWA Shuichi  Keio University, School of Medicine, Research associate, 医学部, 助手 (30231872)

Project Period (FY) 1999 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥45,700,000 (Direct Cost: ¥45,700,000)
Fiscal Year 2003: ¥10,000,000 (Direct Cost: ¥10,000,000)
Fiscal Year 2002: ¥10,000,000 (Direct Cost: ¥10,000,000)
Fiscal Year 2001: ¥8,400,000 (Direct Cost: ¥8,400,000)
Fiscal Year 2000: ¥8,400,000 (Direct Cost: ¥8,400,000)
Fiscal Year 1999: ¥8,900,000 (Direct Cost: ¥8,900,000)
Keywordsmedaka genome / BAC / LG22 / 4D-PCR / sex-determination / GSS / BAC-end sequence / positional cloning / メダカ / HNI / Hd-rR / ゲノム解析 / DMY / DMRT1Y / STS / ゲノムシーケンス / 遺伝子地図 / BACライブラリー / 高密度レプリカメンブレン / 末端シーケンス / BACコンティグ / デジタルハイブリダイゼーション / ケツムライブラリー / pBAC-Lac / EST
Research Abstract

1. We have constructed a set of high-quality Medaka genome BAC library from the inbred HNI strain. About 96,000 clones with average insert size of 160 kb cover 20 times the medaka genome. These clones were individually stocked in 250 of 384-well plates. These clones were also spotted on nylon membranes for colony hybridization screening.
2. We have established a novel procedure to efficiently obtain BAC-end sequences, in which the BAC-DNAs are prepared with 96-well format using Qiagen R.E.A.L. Prep 96 and are sequenced directly by ABI3700/3730 capillary sequencers. We have finished the end-sequencing of 11, 904 Hd-rR BAC clones, 8,160 HNI BAC clones, and 1,152 Cab BAC clones. The total 42,432 end sequence data were deposited in our database as GSS (Genome survey sequence).
3. We also established the two step four dimensional (4D-)PCR screening system for the Hd-rR BAC library. First screening is against superpools each consisting of 1,536 BAC clones. Then, second screening is against the positive superpools identified by the first screening. Individual clones of each superpool are addressed 4-dimensionally, therefore we can identify single clone from the l,536 clones by PCR reactions for 28 second pools. We have prepared twenty superpools, therefore total 30,720 clones are accessible which correspond to 8 times of Medaka genome. A set of screening can be finished within a day.
4. We started entire sequencing of the medaka LG22 chromosome (about 20 Mb) in collaboration with several research groups in the MGI. We have covered 11Mb of genomic region with BAC contigs and have finished sequencing 7Mb of the chromosome.
5. To date, we provided many BAC clones, materials for screenings, and BAC-end sequence data to several research groups. It is noted that the BAC libraries have contributed positional cloning of several genes including medaka sex determining gene and analysis of gene structure as well as constructions of genome-wide BAC contig map and linkage map.

Report

(6 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • 1999 Annual Research Report
  • Research Products

    (37 results)

All Other

All Publications (37 results)

  • [Publications] Yao, Y.: "Genomic structure and expression of the soluble guanylyl cyclase alpha2 subunit gene in the medaka fish Oryzias latipes"Zoological Science. 20. 1293-1304 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okubo, K.: "A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes : evolutionary and functional implications."Gene. 314. 121-131 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, M.: "Absence of the candidate male sex-determining gene dmrtlb(Y) of medaka from other fish species."Current Biology. 13. 416-420 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, M.: "Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus."Gene. 295. 213-222 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nanda, I.: "A duplicated copy of DMRTI in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes."Proc Natl Acad Sci USA. 99. 11778-11783 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okubo, K.: "Structural characterization of GnRH loci in the medaka genome."Gene. 293. 181-189 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Matsuda, M.: "DMY is a Y-specific DM-domain gene required for male development in the medaka fish."Nature. 417. 559-563 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Matsuo M.Y.: "Nucleotide sequence of the MHC class I genomic region of a teleost, the medaka (Oryzias latipes)."Immunogenetics. 53. 930-940 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, S.: "The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor."Current Biology. 11. 1202-1206 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yao Y, Yamamoto, T., Tsutsumi, M., Matsuda, M., Hori, H., Naruse, K., Mitani, H., Shima, A., Asakawa, S., shimizu, N., Suzuki, N.: "Genomic structure and expression of the soluble guanylyl cyclase alpha2 subunit gene in the medaka fish Oryzias latipes."Zoolog Sci. 20. 1293-1304 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okubo, K., Ishii, S., Ishida, J., Mitani, H., Naruse, K., Kondo, M., Shima, A., Tanaka, M., Asakawa, S., Shimizu, N., Aida, K.: "A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes : evolutionary and functional implications."Gene. 314. 121-131 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, M., Nanda, I., Hornung, U., Asakawa, S., Shimizu, N., Mitani, H., Schmid, M., Shima, A., Schartl, M.: "Absence of the candidate male sex-determining gene dmrt1b (Y) of medaka from other fish species."Curr Biol.. 13. 416-420 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, M., Froschauer, A., Kitano, A., Nanda, I., Hornung, U., Volff, J., Asakawa, S., Mitani, H., Naruse, K., Tanaka, M., Schmid, M., Shimizu, N., Schart, M., Shima, A.Tanaka, M., Schmid, M., Shimizu, N., Schartl, M., Shima, A.: "Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus."Gene. 295. 213-222 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C., Shimizu, A., Shan, Z., Haaf, T., Shimizu, N., Shima, A., Schmid, M., Schartl, M.: "A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes."Proc Natl Acad Sci U S A. 99. 11778-11783 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okubo, K., Mitai, H., Naruse, K., Kondo, M., Shima, A., Tanaka, M., Asakawa, S., Shimizu, N., Yoshiura, Y., Aida K.: "Structural characterization of GnRH loci in the medaka genome."Gene. 293. 181-189 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Matsuda, M., Nagahama, Y., Shinomiya, A., Sato, T., Matsuda, C., Kobayashi, T., Morrey, CE., Shibata, N., Asakawa, S., Shimizu, N., Hori, H., Hamagauchi, S., Sakaizumi, M.: "DMY is a Y-specific DM-domain gene required for male development in the medaka fish."Nature. 417. 559-563 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Matsuo MY, Asakawa, S., Shimizu, N., Kimura H, Nonaka M.: "Nucleotide sequence of the MHC class I genomic region of a teleost, the medaka (Oryzias latipes)."Immunogenetics. 53. 930-940 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kondo, S.Kuwahaa, Y., Kondo, M., Naruse, K., Mitani, H., Wakamatsu, Y., Ozato, K., Asakawa, S., Shimizu, N., Shima, A.: "The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor"Curr Biol. 11. 1202-1206 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yao Y, Yamamoto, T., Tsutsumi, M., Matsuda, M., Hori, H., Naruse, K., Mitani, H., Shima, A., Asakawa, S., Shimizu, N., Suzuki, N.: "Genomic structure and expression of the soluble guanylyl cyclase alpha2 subunit gene in the medaka fish Oryzias latipes."Zoolog Sci.. 20. 1293-1304 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Okubo, K., Ishii, S., Ishida, J., Mitani, H., Naruse, K., Kondo, M., Shima, A., Tanaka, M., Asakawa, S., Shimizu, N., Aida, K.: "A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes : evolutionary and functional implications."Gene.. 314. 121-131 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Kondo, M., Nanda, I., Hornung, U., Asakawa, S., Shimizu, N., Mitani, H., Schmid, M., Shima, A., Schartl, M.: "Absence of the candidate male sex-determining gene dmrt1b(Y) of medaka from other fish species."Curr Biol.. 13. 416-420 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, Kobayashi T, Morrey CE, Shibata N, Asakawa S, Shimizu N, Hori H, Hamaguchi S, Sakaizumi M.: "DMY is a Y-specific DM-domain gene required for male development in the medaka fish"Nature. 417. 559-563 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Nanda I, Kondo M, Hornung U, Asakawa S, Winkler C, Shimizu A, Shan Z, Haaf T, Shimizu N, Shima A, Schmid M, Schartl M.: "A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes"Proc. Natl. Acad. Sci. USA. 99. 11778-11783 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Kondo M, Froschauer A, Kitano A, Nanda I, Hornung U, Volff JN, Asakawa S, Mitani H, Naruse K, Tanaka M, Schmid M, Shimizu N, Schartl M, Shima A.: "Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus"Gene. 295. 213-222 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Kondo M, Nanda I, Hornung U, Asakawa S, Shimizu N, Mitani H, Schmid M, Shima A, Schartl M.: "Absense of the Candidate Male Sex-Determining Gene dmrt1b(Y) of Medaka from Other Fish Species"Curr. Biol.. 13. 416-420 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Kondo S.: "The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor"Current Biology. 11・15. 1202-1206 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Kondo M.: "Molecular cloning and characterization of DMRT genes from Medaka Oryzias latipes and the platyfish Xiphophorus maculatus"Gene. (in press).

    • Related Report
      2001 Annual Research Report
  • [Publications] The chromosome 21 mapping and sequencing consortium.: "The DNA sequence of human chromosome 21."Nature. 405. 311-319 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Scott HS et al.: "Insertion of beta-satellite repeats identifies a transmembrane protease causing both congenital and childhood onset autosomal recessive deafness."Nature Genetics. 27. 59-63 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Internation Human Genome Sequencing Consortium: "Initial sequencing and analysis of the human genome."Nature. 409. 860-921 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] International Human Genome Mapping Consortium: "A physical map of the human genome、"Nature. 409. 934-940 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Suzuki K.: "Construction and evaluation of a porcine bacterial artificial library"Anim. Genet.. 31. 8-12 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Dunham I.: "The DNA sequence of human chromosome 22"Nature. 402. 489-501 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Ozaki H.: "Structure and chromosome mapping of the human SLX4 and murine Six4 genes"Cytogenet All Genet.. 87. 108-112 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Gomyo H.: "A 2Mb sequence-ready config map and a novel immunogloblin superfamily gene IGSF4 in the LOH region of chromosome 11823.2"Genomics. 62. 139-146 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Yanauchi T.: "Assignment of the human poly(A) polymerase (PAP) gene to chromosome 14832.1 - 832.2 and isolation of a polymorphic CA reaeat sequence"J. Hum. Genet.. 44. 253-255 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Wu C.: "Construction and charactrization of bacterial artificial chromosome libraries from silkworm Bombyx mori"Mol. Gen. Genet. 261. 698-706 (1999)

    • Related Report
      1999 Annual Research Report

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Published: 1999-04-01   Modified: 2018-03-28  

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