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Analysis of between-species and intra-species diversity using primate genome data and application to conservation biology

Research Project

Project/Area Number 19207008
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biodiversity/Systematics
Research InstitutionNational Institute of Genetics

Principal Investigator

SAITOU Naruya  National Institute of Genetics, 集団遺伝研究系, 教授 (30192587)

Co-Investigator(Kenkyū-buntansha) ISHIDA Takafumi  東京大学, 大学院・理学系研究科, 准教授 (20184533)
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥52,520,000 (Direct Cost: ¥40,400,000、Indirect Cost: ¥12,120,000)
Fiscal Year 2009: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Fiscal Year 2008: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000)
Fiscal Year 2007: ¥34,190,000 (Direct Cost: ¥26,300,000、Indirect Cost: ¥7,890,000)
Keywords霊長類 / DNA多型 / ゲノム解析 / 保全生物学 / 種間交雑 / 遺伝学 / 遺伝子 / ゲノム / 進化 / 人類学
Research Abstract

For primate conservation biology and for intraspecies diversity study, we developed database called "Prim-Prim". Through comparison of human and macaque genomic sequences, intronic regions sandwitched with identical exonic sequences between two species were extracted, and 2,303 primer pairs which can amplify DNA fragment of unsequenced primate genomes were listed in this database, and it is open to public. We used these primers to determine nucleotide sequences of 6 gibbon species, and showed usefulness of these primers.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (51 results)

All 2010 2009 2008 2007 Other

All Journal Article (29 results) (of which Peer Reviewed: 27 results) Presentation (12 results) Book (3 results) Remarks (7 results)

  • [Journal Article] Variations in the coding region of the agouti signaling protein gene do not explain agouti/non-agouti phenotypes in macaques.2010

    • Author(s)
      Nakayama, K., Shotake, T., Takenaka, O., Ishida, T.
    • Journal Title

      Journal of Mammalian Evolution (in press)

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Study of cynomolgus monkey (Macaca fascicularis) DRA polymorphism in four populations.2010

    • Author(s)
      Aarnink A., Estrade L., Apoil P.A., Kita Y.F., Saitou N., Shiina T., Blancher A.
    • Journal Title

      Immunogenetics 62(3)

      Pages: 123-136

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera.2010

    • Author(s)
      Matsudaira, K., Ishida, T.
    • Journal Title

      Molecular Phylogenetics and Evolution 55

      Pages: 454-459

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Variations in the coding region of the agouti signaling protein gene donot explain agouti/non-agouti phenotypes in macaques2010

    • Author(s)
      Nakayama, K.
    • Journal Title

      Journal of Mammalian Evolution (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A hypervariable STR polymorphism in the complement factor I(CFI)gene : Asian-specific alleles2010

    • Author(s)
      Yuasa I.
    • Journal Title

      International Journal of Legal Medicine (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera2010

    • Author(s)
      Matsudaira, K.
    • Journal Title

      Molecular Phylogenetics and Evolution 55

      Pages: 454-459

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis.2009

    • Author(s)
      Kitano T., Noda R., Takenaka O., Saitou N.
    • Journal Title

      Molecular Phylogenetics and Evolution 51

      Pages: 465-471

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Variable number of tandem repeat polymorphisms of DRD4: re-evaluation of selection hypothesis and analysis of association with schizophrenia.2009

    • Author(s)
      Hattori E., Nakajima M., Yamada K., Iwayama Y., Toyota T., Saitou N., Yoshikawa T.
    • Journal Title

      European Journal of Human Genetics 17

      Pages: 793-801

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] 霊長類の種内変異を解析するためのPCRプライマーデータベースPrim-Primの開発とその応用.2009

    • Author(s)
      斎藤成也, 鈴木留美子, 河合洋介, 石田貴文
    • Journal Title

      DNA多型 17

      Pages: 63-65

    • NAID

      10025754140

    • Related Report
      2009 Final Research Report
  • [Journal Article] Skewed matrilineal genetic composition in a small wild chimpanzee community.2009

    • Author(s)
      Shimada M.K., Hayakawa S., Fujita S., Sugiyama Y., Saitou N.
    • Journal Title

      Folia Primatologica 80(1)

      Pages: 19-32

    • NAID

      130006997736

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] HERC1 polymorphisms : population-specific variations in haplotype composition2009

    • Author(s)
      Yuasa I.
    • Journal Title

      Cell Biochemistry and Function 27

      Pages: 402-405

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Variable number of tandem repeat polymorphisms of DRD4 re-evaluation of selection hypothesis and analysis of association with schizophrenia2009

    • Author(s)
      Hattori E.
    • Journal Title

      European Journal of Human Genetics 17

      Pages: 793-801

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ヒトゲノム研究の新しい地平2009

    • Author(s)
      斎藤成也
    • Journal Title

      Anthropological Science 117

      Pages: 1-9

    • NAID

      10029570649

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 霊長類の種内変異を解析するためのPCRプライマーデータベース Prim-Prim の開発とその応用2009

    • Author(s)
      斎藤成也
    • Journal Title

      DNA多型 17

      Pages: 63-65

    • NAID

      10025754140

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Mitochondrial DNA sequence phylogeny of four populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis).2008

    • Author(s)
      Blancher A., Bonhomme M., Crouau-Roy B., Terao K., Kitano T., Saitou N.
    • Journal Title

      Journal of Heredity 99(3)

      Pages: 254-264

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Natural selection in the TRL-related genes in the course of primate evolution.2008

    • Author(s)
      Nakajima, T., Ohtani, H., Satta, Y., Uno, Y., Akari, H., Ishida, T., Kimura, A.
    • Journal Title

      Immunogenetics 60

      Pages: 727-735

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Variation of the melanocortin 1 receptor gene in the macaques.2008

    • Author(s)
      Nakayama, K., Shotake, T., Takenaka, O., Ishida, T.
    • Journal Title

      American Journal of Primatology 70

      Pages: 778-785

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies.2008

    • Author(s)
      Liu Y.-H., Takahashi A., Kitano T., Koide T., Shiroishi T., Moriwaki K., Saitou N.
    • Journal Title

      Genes and Genetic Systems 83

      Pages: 77-88

    • NAID

      10024395628

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mitochondrial DNA sequence phylogeny of four populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis)2008

    • Author(s)
      Blancher A.
    • Journal Title

      Journal of Heredity 99 (3)

      Pages: 254-264

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Natural selection in the TRL-related genes in the course of primate evolution2008

    • Author(s)
      Nakajima T.
    • Journal Title

      Immunogenetics 60

      Pages: 727-735

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Variation of the melanocortin 1 receptor gene in the macaques2008

    • Author(s)
      Nakayama K.
    • Journal Title

      American Journal of Primatology 70

      Pages: 778-785

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Skewed Matrilineal Genetic Composition in a Small Wild Chinpanzee Community2008

    • Author(s)
      Shimada M. K.
    • Journal Title

      Folia Primatologica 80 (1)

      Pages: 19-32

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular basis of complement factor I (CFI)polymorphism : one of two polymorphic suballeles responsible for CFI A is Japanese-specific2008

    • Author(s)
      Yuasa I.
    • Journal Title

      Journal of Human Genetics 53

      Pages: 1016-1021

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mitochondrial DNA sequence phylogeny of four populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis)2008

    • Author(s)
      Blancher A.
    • Journal Title

      Journal of Heredity 99(3)

      Pages: 254-264

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies2008

    • Author(s)
      Liu Y.-H.
    • Journal Title

      Genes and Genetic Systems 83

      Pages: 77-88

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] TP53 codon 72 polymorphism in 12 populations of insular Southeast Asia and Oceania2007

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

      Journal of Human Genetics 52

      Pages: 694-697

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] FTO polymorphisms in Oceanic populations2007

    • Author(s)
      Ohashi, J., et. al.
    • Journal Title

      Journal of Human Genetics 52

      Pages: 1031-1035

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative analysis of cell-free Epstein-Barr virus DNA in the plasma of patients with peripheral T-cell and NK-cell lymphomas and peripheral T-cell proliferative diseases.2007

    • Author(s)
      Suwiwat, S., et. al.
    • Journal Title

      Journal of Clinical Virology 40

      Pages: 277-283

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Variable number of tandem repeat polymorphisms of DRD4 : re-evaluation of selection hypothesis and analysis of association with schizophrenia

    • Author(s)
      Hattori E.
    • Journal Title

      European Journal of Human Genetics (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 遺伝子から見る人類進化2009

    • Author(s)
      斎藤成也
    • Organizer
      日本遺伝学会第81回大会
    • Place of Presentation
      松本市
    • Year and Date
      2009-09-16
    • Related Report
      2009 Annual Research Report
  • [Presentation] 霊長類の種内変異を解析するためのPCRプライマーデータベースPrim-Primの開発とその応用2008

    • Author(s)
      斎藤成也
    • Organizer
      日本DNA多型学会第17回学術集会
    • Place of Presentation
      東京
    • Year and Date
      2008-11-21
    • Related Report
      2009 Final Research Report
  • [Presentation] 霊長類の種内変異を解析するためのPCRプライマーデータベースPrim-PrimDBの開発とその応用2008

    • Author(s)
      斎藤成也
    • Organizer
      日本DNA多型学会第17回学術集会
    • Place of Presentation
      東京
    • Year and Date
      2008-11-21
    • Related Report
      2008 Annual Research Report
  • [Presentation] 霊長類ゲノム多様性解析のためのPrim-Prim DBの開発とその応用2008

    • Author(s)
      斎藤成也
    • Organizer
      日本人類学会第62回大会
    • Place of Presentation
      名古屋市
    • Year and Date
      2008-11-01
    • Related Report
      2009 Final Research Report
  • [Presentation] 霊長類ゲノム多様性解析のためのPrim-Prim DBの開発とその応用2008

    • Author(s)
      斎藤成也
    • Organizer
      日本人類学会第62回大会
    • Place of Presentation
      名古屋
    • Year and Date
      2008-11-01
    • Related Report
      2008 Annual Research Report
  • [Presentation] トコンドリアゲノム配列を用いたHylobatesとSymphalangusの分岐年代推定2008

    • Author(s)
      松平一成, 石田貴文
    • Organizer
      日本霊長類学会
    • Place of Presentation
      東京
    • Year and Date
      2008-07-05
    • Related Report
      2009 Final Research Report
  • [Presentation] ミトコンドリアゲノム配列を用いたHylobatesとSymphalangusの分岐年代推定2008

    • Author(s)
      松平一成
    • Organizer
      日本霊長類学会
    • Place of Presentation
      東京
    • Year and Date
      2008-07-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] Utility of phylogenetic network for deciphering nucleotide sequence history2008

    • Author(s)
      Saitou N
    • Organizer
      NIG International Symposium
    • Place of Presentation
      東京
    • Year and Date
      2008-03-28
    • Related Report
      2009 Final Research Report
  • [Presentation] Utility of phylogenetic network for deciphering nucleotide sequence history2008

    • Author(s)
      Saitou N.
    • Organizer
      NIG International Symposium
    • Place of Presentation
      National Institute of Informatics, Tokyo
    • Year and Date
      2008-03-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] Evolutionary analysis on primates2007

    • Author(s)
      Saitou N
    • Organizer
      79th Annual Meeting of the Genetics Society of Japan
    • Place of Presentation
      岡山市
    • Year and Date
      2007-09-21
    • Related Report
      2009 Final Research Report
  • [Presentation] Evolutionary analysis on primates2007

    • Author(s)
      Saitou N.
    • Organizer
      79th Annual Meeting of the Genetics Society of Japan
    • Place of Presentation
      Okayama University, Okayama
    • Year and Date
      2007-09-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] Neccessity of Non-Tree Structure in Nuclear DNA Phylogeny2007

    • Author(s)
      Saitou N.
    • Organizer
      Symposium on Species Diversity
    • Place of Presentation
      Lassa, Tibet, China
    • Year and Date
      2007-06-08
    • Related Report
      2007 Annual Research Report
  • [Book] 絵でわかる人類の進化2009

    • Author(s)
      斎藤成也
    • Total Pages
      192
    • Publisher
      講談社サイエンティフィック
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Book] ゲノム進化学入門2007

    • Author(s)
      斎藤成也
    • Total Pages
      257
    • Publisher
      共立出版
    • Related Report
      2009 Final Research Report
  • [Book] ゲノム進化学入門2007

    • Author(s)
      斎藤 成也
    • Total Pages
      257
    • Publisher
      共立出版
    • Related Report
      2007 Annual Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/index-j.htmlhttp://sayer.lab.nig.ac.jp/~saitou/index-j.html

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/index-j.html

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/~saitou/index-j.html

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://saver.lab.nig.ac.jp/index-j.html

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/~saitou/index-j.html

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/index-j.html

    • Related Report
      2007 Annual Research Report
  • [Remarks]

    • URL

      http://sayer.lab.nig.ac.jp/~saitou/index-j.html

    • Related Report
      2007 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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