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Integrative study of nucleotide sequence evolution using primate genomes as model

Research Project

Project/Area Number 26251040
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Evolutionary biology
Research InstitutionNational Institute of Genetics

Principal Investigator

SAITOU NARUYA  国立遺伝学研究所, 集団遺伝研究系, 教授 (30192587)

Co-Investigator(Kenkyū-buntansha) 池尾 一穂  国立遺伝学研究所, 生命情報研究センター, 准教授 (20249949)
太田 聡史  国立研究開発法人理化学研究所, バイオリソースセンター, 専任研究員 (30391890)
長田 直樹  北海道大学, 情報科学研究科, 准教授 (70416270)
古賀 章彦  京都大学, 霊長類研究所, 教授 (80192574)
北野 誉  茨城大学, 工学部, 准教授 (90400564)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥40,950,000 (Direct Cost: ¥31,500,000、Indirect Cost: ¥9,450,000)
Fiscal Year 2016: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
Fiscal Year 2015: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2014: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Keywordsゲノム進化 / 霊長類 / CNS / 反復配列 / カニクイザル / Rh式血液型遺伝子 / チベットモンキー / 突然変異パターン / 遺伝子変換 / ABO式血液型遺伝子 / ゲノム解析 / カピバラ / ムササビ / 比較ゲノム / 突然変異 / ゲノム / 進化 / 哺乳類
Outline of Final Research Achievements

Evolutionarily conserved noncoding sequences (CNSs) were analyzed for whole Eukaryotes, Amniotes, Hominoids, and Hominidae by comparing many genome sequences, and series of new CNS characteristics were discovered (mainly conduced by Saitou). Repeat sequence evolution of New World monkeys were analyzed (mainly conduced by Koga). Genomic structure of chimpanzee Rh blood group gene region was analyzed (mainly conduced by Kitano). Whole-genome sequences of Mauritian cynomolgus macaques and Tibetan macaque were analyzed (mainly conduced by Osada). Substitution type mutation pattens were analyzed by using ENU-induced mice (mainly conduced by OOta). Gene annotation of cynomolgus macaque genome was conducted (mainly conduced by Ikeo). These studies deciphered various facets of genome evolution, in particular, of primates.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (36 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (19 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 19 results,  Open Access: 13 results,  Acknowledgement Compliant: 6 results) Presentation (14 results) (of which Invited: 5 results) Book (2 results)

  • [Int'l Joint Research] Universite´ Paul Sabatier, Toulouse III(France)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] DNA analyses of camels2017

    • Author(s)
      Saitou N. and Shokat S.
    • Journal Title

      Journal of Arid Land Studies

      Volume: 26 Pages: 223-226

    • NAID

      130005640911

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences.2017

    • Author(s)
      Suzuki A, Komata H, Iwashita S, Seto S, Ikeya H, Tabata M, Kitano T.
    • Journal Title

      Molecular Phylogenetics and Evolution

      Volume: 107 Pages: 1-9

    • DOI

      10.1016/j.ympev.2016.10.004

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Translational repression of a splice variant of cynomolgus macaque CXCL1L by its C-terminal sequence2017

    • Author(s)
      Hisayuki Nomiyama, Naoki Osada, Ichiro Takahashi, Keiji Terao, Kazuya Yamagata, Osamu Yoshie
    • Journal Title

      J. Interferon Cytokine Res.

      Volume: 37 Pages: 129-138

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] GC content heterogeneity transition of conserved noncoding sequences occurred at the emergence of vertebrates2016

    • Author(s)
      Hettiarachchi N. and Saitou N.
    • Journal Title

      Genome Biology and Evolution

      Volume: 8 Issue: 11 Pages: 3377-3392

    • DOI

      10.1093/gbe/evw231

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Emergence and evolution of Hominidae-specific coding and noncoding genomic sequences2016

    • Author(s)
      Saber M. M., Babarinde I. A., Hettiarachchi N., and Saitou N.
    • Journal Title

      Genome Biology and Evolution

      Volume: 8 Issue: 7 Pages: 2076-2092

    • DOI

      10.1093/gbe/evw132

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Formation of functional CENP-B boxes at diverse locations in repeat units of centromeric DNA in New World monkeys.2016

    • Author(s)
      Kugou K, Hirai H, Masumoto H, Koga A.
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 27833-27833

    • DOI

      10.1038/srep27833

    • NAID

      120005818231

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] No distinction of orthology/paralogy between human and chimpanzee Rh blood group genes2016

    • Author(s)
      Babarinde I. A. and Saitou N
    • Journal Title

      Molecular Biology and Evolution

      Volume: msw058 Issue: 7 Pages: 1807-1817

    • DOI

      10.1093/molbev/msw058

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] No distinction of orthology/paralogy between human and chimpanzee Rh blood group genes.2016

    • Author(s)
      Kitano T., Kim C.-G., Blancher A., and Saitou N.
    • Journal Title

      Genome Biology and Evolution

      Volume: 8 Issue: 3 Pages: 519-527

    • DOI

      10.1093/gbe/evw022

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] CENP-B box, a nucleotide motif involved in centromere formation, occurs in a New World monkey2016

    • Author(s)
      Suntronpong A, Kugou K, Masumoto H, Srikulnath K, Ohshima K, Hirai H, *Koga A
    • Journal Title

      Biology Letters

      Volume: 12 Issue: 3 Pages: 20150817-20150817

    • DOI

      10.1098/rsbl.2015.0817

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genetic diversity in humans and non-human primates and its evolutionary consequences2015

    • Author(s)
      Naoki Osada
    • Journal Title

      Genes & Genetic Systems

      Volume: 90 Issue: 3 Pages: 133-145

    • DOI

      10.1266/ggs.90.133

    • NAID

      130005105460

    • ISSN
      1341-7568, 1880-5779
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Higher-order repeat structure in alpha satellite DNA occurs in New World monkeys and is not confined to hominoids2015

    • Author(s)
      Penporn Sujiwattanarat, Watcharaporn Thapana, Kornsorn Srikulnath, Yuriko Hirai, Hirohisa Hirai, Akihiko Koga
    • Journal Title

      Scientific Reports

      Volume: 14 Issue: 1 Pages: 10315-10315

    • DOI

      10.1038/srep10315

    • NAID

      120005758209

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] CYP2D44 polymorphisms in cynomolgus and rhesus macaques2015

    • Author(s)
      3.Yasuhiro Uno*, Shotaro Uehara, Sakae Kohara, Naoki Osada, Norie Murayama, Hiroshi Yamazaki.
    • Journal Title

      Mol. Biol. Rep.

      Volume: 印刷中

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck.2015

    • Author(s)
      Osada N., Hettiarachchi N., Babarinde I., Saitou N., Blancher A
    • Journal Title

      Genome Biology and Evolution

      Volume: 7 Issue: 3 Pages: 821-830

    • DOI

      10.1093/gbe/evv033

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Asian DNA Repository Consortium. Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data2015

    • Author(s)
      5.Shigeki Nakagome, Takehiro Sato, Hajime Ishida, Tsunehiko Hanihara, Tetsutaro Yamaguchi, Ryosuke Kimura, Shuhei, Mano, Hiroki Oota
    • Journal Title

      Mol. Biol. Evol

      Volume: 印刷中

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reduction in the structural instability of cloned eukaryotic tandem-repeat DNA by low-temperature culturing of host bacteria2014

    • Author(s)
      Watcharaporn Thapana, Penporn Sujiwattanarat, Kornsorn Srikulnath, Hirohisa Hirai, and Akihiko Koga
    • Journal Title

      Genetics Research

      Volume: 96

    • DOI

      10.1017/s0016672314000172

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes2014

    • Author(s)
      Baicharoen S, Miyabe-Nishiwaki T, Arsaithamkul V, Hirai Y, Duangsa-ard K, Siriaroonrat B, Domae H, Srikulnath K, Koga A, *Hirai H
    • Journal Title

      PLOS ONE

      Volume: 9 Issue: 10 Pages: e109151-e109151

    • DOI

      10.1371/journal.pone.0109151

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Novel variable number of tandem repeats of gibbon MAOA gene and its evolutionary significance2014

    • Author(s)
      Y. Choi, Y.-D. Jung, S. Ayarpadikannan, A. Koga, H. Imai, H. Hirai, C. Roos,and H.-S. Kim
    • Journal Title

      Genome

      Volume: 57 Issue: 8 Pages: 427-432

    • DOI

      10.1139/gen-2014-0065

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Extracting population genetics information from a diploid genome sequence2014

    • Author(s)
      Naoki Osada
    • Journal Title

      Front. Ecol. Evol.

      Volume: 2 Pages: 7-7

    • DOI

      10.3389/fevo.2014.00007

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The genome landscape of the African green monkey kidney-derived Vero cell line.2014

    • Author(s)
      Osada N, Kohara A, Yamaji T, Hirayama N, Kasai F, Sekizuka T, Kuroda M, Hanada K
    • Journal Title

      DNA Res.

      Volume: 21 Issue: 6 Pages: 673-683

    • DOI

      10.1093/dnares/dsu029

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Evolutionary history and roles of conserved non-coding sequences in eukaryotes.2016

    • Author(s)
      Saitou N.
    • Organizer
      KAUST Research Conference: Computational Systems Biology in Biomedicine
    • Place of Presentation
      KAUST, Saudi Arabia
    • Year and Date
      2016-12-21
    • Related Report
      2016 Annual Research Report
  • [Presentation] Population genomics of non-human primates: a case of Mauritian cynomolgus macaques (Macaca fascicularis). Naoki Osada, Soichi Sakurai2016

    • Author(s)
      Osada N.
    • Organizer
      5th Asian Primate Symposium
    • Place of Presentation
      Sri Jayewardenepura, Sri-Lanka
    • Year and Date
      2016-10-20
    • Related Report
      2016 Annual Research Report
  • [Presentation] セントロメア反復配列の急速な入れ替わり:テナガザルとヨザルの例2016

    • Author(s)
      古賀章彦、平井啓久
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Evolutionarily conserved noncoding sequence in eukaryotes2016

    • Author(s)
      Saitou N.
    • Organizer
      The 14th CJK Bioinformatics Training Course & Symposium
    • Place of Presentation
      Amoi, China
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] ヒトのABO式血液型遺伝子における組換えの解析2014

    • Author(s)
      伊藤正哉,北野誉
    • Organizer
      第37回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(横浜市西区みなとみらい)
    • Year and Date
      2014-11-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] ゲノム重複の起源とその進化上の影響2014

    • Author(s)
      斎藤成也
    • Organizer
      日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(横浜市西区みなとみらい)
    • Year and Date
      2014-11-26
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Characteristics of evolutionarily conserved noncoding sequences (CNSs) in eukaryote genomes2014

    • Author(s)
      Saitou Naruya
    • Organizer
      International Conference on Evolutionary Genomics and Bioinformatics
    • Place of Presentation
      國立成功大学(Tainan City, 台湾 )
    • Year and Date
      2014-11-08
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] DNA-based transposable elements as natural mutators in vertebrate genomes2014

    • Author(s)
      Akihiko Koga
    • Organizer
      2014 International Conference of the Korean Society for Molecular and Cellular Biology
    • Place of Presentation
      COEX (Seoul, Korea)
    • Year and Date
      2014-10-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 真核生物ゲノムにおける 進化的に保存された タンパク質非コード領域の特徴2014

    • Author(s)
      斎藤成也
    • Organizer
      日本遺伝学会第86回大会
    • Place of Presentation
      長浜バイオ大学(滋賀県長浜市)
    • Year and Date
      2014-09-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Characteristics of evolutionarily conserved protein noncoding regions in eukaryote genomes2014

    • Author(s)
      Saitou Naruya
    • Organizer
      Otto Warburg International Summer School and Research Symposium on Comparative and Evolutionary Genomics
    • Place of Presentation
      SIBS(Shanghai 中国)
    • Year and Date
      2014-09-15
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 系統ネットワーク法を用いたヒトABO式血液型遺伝子の解析2014

    • Author(s)
      伊藤正哉,北野誉
    • Organizer
      日本進化学会第16回大阪大会
    • Place of Presentation
      高槻現代劇場(大阪府高槻市)
    • Year and Date
      2014-08-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] Higher-order repeat structure in centromeric repetitive DNA is not confined to central regions2014

    • Author(s)
      Penporn Sujiwattanarat, Watcharaporn Thapana, Kornsorn Srikulnath, 平井啓久, 古賀章彦
    • Organizer
      日本進化学会第16回大阪大会
    • Place of Presentation
      高槻現代劇場(大阪府高槻市)
    • Year and Date
      2014-08-21
    • Related Report
      2014 Annual Research Report
  • [Presentation] Incredible gibbon alpha-satellite: evolutionary origin of higher-order repeat structure2014

    • Author(s)
      Akihiko Koga, Yuriko Hirai, Israt Jahan, Sudarath Baicharoen, Visit Arsaithamkul, Hirohisa Hirai H
    • Organizer
      25th International Primatological Society Congress
    • Place of Presentation
      Melia Hanoi Hotel (Hanoi, Vietnam)
    • Year and Date
      2014-08-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] ヨザルの染色体変異に関与したと考えられる大規模反復配列2014

    • Author(s)
      古賀章彦, Ornjira Prakhongcheep, Nampech Chaiprasertsri, 平井百合子, 平井啓久
    • Organizer
      第30回日本霊長類学会大会
    • Place of Presentation
      大阪科学技術センター(大阪市西区)
    • Year and Date
      2014-07-05
    • Related Report
      2014 Annual Research Report
  • [Book] 歴誌主義宣言2016

    • Author(s)
      斎藤成也
    • Total Pages
      207
    • Publisher
      ウェッジ
    • Related Report
      2015 Annual Research Report
  • [Book] ビッグデータ時代のゲノミクス情報処理2014

    • Author(s)
      北上始・斎藤成也・太田聡史
    • Total Pages
      226
    • Publisher
      コロナ社
    • Related Report
      2014 Annual Research Report

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Published: 2014-04-04   Modified: 2018-03-22  

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