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Elucidation of the machinery of biodiversity on the basis of evolutionary genetics

Research Project

Project/Area Number 10836024
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 自然史科学
Research InstitutionNational Institute of Genetics

Principal Investigator

GOJOBORI Takashi  National Institute of Genetics, Center for Information Biology, Professor, 生命情報研究センター, 教授 (50162136)

Co-Investigator(Kenkyū-buntansha) IMANISHI Tadashi  National Institute of Genetics, Center for Information Biology, Assistant Professor, 生命情報研究センター, 助手 (80270461)
Project Period (FY) 1998 – 1999
Project Status Completed (Fiscal Year 1999)
Budget Amount *help
¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 1999: ¥1,300,000 (Direct Cost: ¥1,300,000)
Fiscal Year 1998: ¥2,100,000 (Direct Cost: ¥2,100,000)
Keywordsevolution / biodiversity / complete genome sequences / genome duplication MHC / hitchhiking effect / operon / GC-content / GC含量 / ゲノム / 大量解析 / 重複領域 / データベース / 系統樹
Research Abstract

In this research project, from the viewpoint of evolutionary genetics we attempted to elucidate biodiversity that living organisms have acquired through evolution since the beginning of 3.5 billion years ago. Currently, a lot of complete genome sequences from a variety of species such as human are available, and hundreds of genome-sequencing projects are thought to be underway. Thus, these genomes gave us an opportunity to initiate the project of biodiversity analysis.
In the first academic year we conducted detection of duplicated regions in eukaryotic genomes such as human. In order to improve the accuracy of the detection, we developed a new statistical method of finding significant duplicated regions. Consequently, we successfully identified 74 duplicated regions in human, 59 in yeast, and 197 in worm. We constructed a database for these results, so that anyone can access our data through Internet by using a graphical user interface. The times of duplication events were estimated so as to study what the duplication affect to evolution.
In the second academic year, in order to analyze the MHC region of human in detail, a large DNA sequence (〜400 kb) in the region was newly determined. As a result, we found large genome duplication, and reconstructed the evolutionary process of the duplication. Moreover, high nucleotide diversity was found in non-coding regions, implying that hitchhiking effects might have occurred in the regions. Next, we extended our study to microbes, and could reveal that in general bacterial genome structures are quite unstable even in operons that are believed to be functionally important units. In addition, we developed a new method for the detection of evolutionary direction of GC-content change, which leads to high diversity of genomes.

Report

(3 results)
  • 1999 Annual Research Report   Final Research Report Summary
  • 1998 Annual Research Report
  • Research Products

    (44 results)

All Other

All Publications (44 results)

  • [Publications] Bellgard, M.: "Significant differences between the G+C content of synonymous codons in orthologous genes the genomic G+C content"Gene Special Issue.. 238・1. 33-37 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Gaudieri, S.: "Extensive nucleotide variability in a 370kb sequence within the central region of the major histocompatibility complex"Gene Special Issue.. 238・1. 157-161 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Baba, T.: "Isolation and characterization of a pig major histocompatibility complez(SLA) class II DNA cDNA clone"Immunogenetics. 49. 915-917 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Gaudieri, S.: "Different Evolutionary histories in two subgenomic regions of the major histocompatibility complex"Genome Research.. 9・6. 541-549 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Bellgard, M.: "Inferring the direction of evolutionary changes of genomic base composition"Trends in Genetics. 15・7. 254-256 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Itoh, T.: "A low rate of nucleotide changes in Escherichia coil K-12 estimated from a comparison of the genome sequences between two different substrains"FEBS Letters. 450. 72-76 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Gaudieri, S.: "Nucleotide diversity within the human major histocompatibility complex : Function of hitch-hiking effect, duplications, indels and recombination"6th International workshop on MHC evolution. Hayama. 186-200 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Shiina, T.: "Multiple class I loci expressed by the quail MHC"Immunogenetics.. 49・5. 456-460 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Itoh, T.: "Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes"Mol. Biol. Evol.. 16・3. 332-346 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Hatta, T.: "HLA genomes and haplotypes in Ryukyuan suggest a recent gene flow to the Okinawa islands"Human Biology. 71.3. 353-365 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Shiina, T.: "Gene organization of the quail major histocompatibility complex (MhcCoja) class I gene region"Immunogenetics. 49.5. 384-394 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Mizuki, N.: "Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China"Tissue Antigens. 51,3. 287-292 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Katuyama, Y.: "Genetic relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, ,Greek, Saudi Arabian and Italian populations based on allelic frequencies at four VNTR(DIS80, D4S43, C0L2A1, D17S5) and one STR(ACTBP2)loci"Human Heredity. 48,3. 126-137 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] 五條堀孝: "つぎはぎだらけの生き物ゲノム"サイアス・朝日新聞出版局. 4・7. 20-23 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Bellgard,M.: "Annals of the New York Academy of Sciences : New York"L.H.caporale,Editor.. 434 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Bellgard, M. and Gojobori, T.: "Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content."Gene. 238(1). 33-37 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Gaudieri, S., Kulski, J.K., Dawkins, R.L., and Gojobori, T: "Extensive nucleotide variability in a 370kb sequence within the central region of the major histocompatibility complex."Gene Special Issue. 238(1). 157-161 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Baba, T., Shiina, T., Ando, A., Imanishi, T., Matsuno, N., Sakurai, E., Nagao, T., Tanaka, K., Gojobori, T., and Inoko, H.: "Isolation and characterization of a pig major histocompatibility complez (SLA) class II DNA cDNA clone."Immunogenetics. 49. 915-917 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Gaudieri, S., Kulski, J., Dawkins, R., and Gojobori, T.: "Different evolutionary histories in two subgenomic regions of the major histocompatibility complex."Genome Research. 9(6). 541-549 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Bellgard, M. and Gojobori, T.: "Inferring the direction of evolutionary changes of genomic base composition."Trends in Genetics.. 15(7). 254-256 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Itoh, T., Okayama, T., Hashimoto, H., Takeda, J.-I., Davis, RW., Mori, H., and Gojobori, T.: "A low rate of nucleotide changes in Escherichia coil K-12 estimated from a comparison of the genome sequences between two different substrains."FEBS Letter.. 450. 72-76 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Shiina, T., Oka, A.,Imanishi, T., Hanzawa, K., Gojobori, T., Watanabe, S., and Inoko, H.: "Multiple class I loci expressed by the quail MHC."Immunogenetics. 49(5). 456-460 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Itoh, T., Takemoto, K., Mori, H., and Gojobori, T.: "Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes."Mol. Biol. Evol.. 16(3). 332-346 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Hatta, Y., Ohashi, J., Imanishi, T., Kamiyama, H., Iha, M., Simabukuro, T., Ogawa, A., Tanaka, H., Akaza, T., Gojobori, T., Juji, T., and Tokunaga, K.: "HLA genes and haplotypes in Ryukyuan suggest a recent gene flow to the Okinawa Islands."Human Biology. 71(3). 353-365 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Shiina, T., Shimizu, C., Oka, A., Teraoka, Y.,Imanishi, T., Gojobori, T., Hanzawa, K., Watanabe, S., and Inoko, H.: "Gene organization of the quail major histocompatibility complex (MhcCoja) class I gene region."

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Mizuki, N., Ohno, S., Ando, H., Sato, T., Imanishi, T., Gojobori, T., Ishihara, M., Goto, K., Ota, M., Geng, Z., Geng, L., Li, G., and Inoko, H.: "Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China."Tissue Antigens. 51(3). 287-292 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Katsuyama, Y., Inoko, H., Imanishi, T., Mizuki, N., Gojobori, T., and Ota, M.: "Genetic relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian and Italian populations based on allelic frequencies at four VNTR (DIS80, D4S43, COL2A1, DI7SS) and one STR (ACTBP2) loci."Human Heredity. 48(3). 126-137 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Bellgard, M.: "Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content"Cene Special Issue (in press).

    • Related Report
      1999 Annual Research Report
  • [Publications] Guadieri, S.: "Extensive nucleotide variability in a 370kb sequence within the central region of the major histocompatibility complex"Gene Special Issue. 238・1. 157-161 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Baba, T.: "Isolation and characterizaation of a pig major histocompatibility complez (SLA) class II DNA cDNA clone"Immunogenetics. 49. 915-917 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Gaudieri, S.: "Different evolutionary histories in two subgenomic regions of the major histocompatibility complex"Genome Research. 9・6. 541-549 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Bellgard, M.: "Inferring the direction of evolutionary changes of genomic base composition"Trends in Genetics. 15・7. 254-256 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Itoh, T.: "A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains"FEBS Letters. 450. 72-76 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Gaudieri, S.: "Nucleotide diversity within the human major histocompatibility complex : Funcition of hitch-hiking effect, duplications, indels and recombination"6th International workshop on MHC evolution. Hayama. 186-200

    • Related Report
      1999 Annual Research Report
  • [Publications] Shiina, T.: "Multiple class I Loci expressed by the quail MHC"Immunogenetics. 49・5. 456-460 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Itoh, T.: "Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes"Mol. Biol. Evol.. 16・3. 332-346 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] 五條堀孝: "つぎはぎだらけの生き物のゲノム"サイアス・朝日新聞出版局. 4・7. 20-23 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Bellgard, M.: "Annals of the New York Academy of Sciences : New York"L.H. Caporale, Editor.. 434 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Hatta,Y.: "HLA genes and haplotypes in Ryukyuan suggest a recent gene flow to the Okinawa islands." Human Biology. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Shiina,T.: "Multiple class I loci expressed by the quail MHC." Immunogenetics. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Bellgard,M.: "Dynamic Evolution of Genomes and the Concept of Genome Space." Annals of the New York Academy of Sciences. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Shiina,T.: "Gene organization of the quail major histocompatibility.complex(MhcCoja)class I gene region." Immunogenetics. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Mizuki,N.: "Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China" Tissue Antigens. 51,3. 287-292 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Katsuyama,Y.: "Genetic relationships among Japanese,Northern Han,Hui,Uygur,Kazakh,Greek,Saudi Arabian and Italian populations based on allelic freouencies at four VNTR(D1S80,D4S43,C0L2A1,D17S5)and one STR(ACTBP2)loci" Human Heredity. 48,3. 126-137 (1998)

    • Related Report
      1998 Annual Research Report

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Published: 1998-04-01   Modified: 2016-04-21  

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