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Analysis of the genome evolution by gene duplication using olfactory receptor gene families

Research Project

Project/Area Number 23770271
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Evolutionary biology
Research InstitutionThe University of Tokyo (2013-2015)
Tokyo Medical and Dental University (2011-2012)

Principal Investigator

Niimura Yoshihito  東京大学, 農学生命科学研究科, 特任准教授 (90396979)

Project Period (FY) 2011-04-28 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywords嗅覚受容体 / 化学感覚 / 遺伝子ファミリー / 比較ゲノム / 分子進化 / 哺乳類の進化 / 化学受容 / 哺乳類 / 遺伝子クラスター / 多重遺伝子族 / カメ / ネットワーク
Outline of Final Research Achievements

Olfaction is essential for the survival of many animals. The ability to distinguish different odors depends on the number and type of olfactory receptors (ORs) present in each organism’s genome. In this project, we examined the OR genes encoded in 13 mammalian species’ genomes and found that African elephants have a surprisingly large number of OR genes, with approximately 2,000. This number is by far the largest among ever characterized. We also invented a novel bioinformatic method to trace the evolutionary trajectories of individual OR genes, and examined their duplications and losses in each species. We then discovered three OR genes that are evolutionarily stable for 100 million years without any duplications and losses and with very little change in sequence. Suggestively, these receptors would have physiologically important functions common to every mammal beyond the detection of odors.

Report

(6 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (50 results)

All 2016 2015 2014 2013 2012 2011 Other

All Journal Article (16 results) (of which Peer Reviewed: 8 results,  Acknowledgement Compliant: 2 results,  Open Access: 2 results) Presentation (27 results) (of which Int'l Joint Research: 4 results,  Invited: 9 results) Book (7 results)

  • [Journal Article] Ligand specificity and evolution of mammalian musk odor receptors: Effect of single receptor deletion on odor detection.2016

    • Author(s)
      Sato-Akuhara N, Horio N, Kato-Namba A, Yoshikawa K, Niimura Y, Ihara S, Shirasu M, Touhara K.
    • Journal Title

      The Journal of Neuroscience

      Volume: in press

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 乳酸により活性化される嗅覚受容体は低酸素状態のセンサーとして機能する2016

    • Author(s)
      新村芳人
    • Journal Title

      細胞工学

      Volume: 35 Pages: 223-223

    • Related Report
      2015 Annual Research Report
  • [Journal Article] においのサイエンス2016

    • Author(s)
      新村芳人
    • Journal Title

      Felicite

      Volume: 2 Pages: 2-9

    • Related Report
      2015 Annual Research Report
  • [Journal Article] 嗅覚受容体遺伝子──その進化と機能の多様性2015

    • Author(s)
      新村芳人
    • Journal Title

      医学のあゆみ

      Volume: 253 Pages: 473-479

    • Related Report
      2015 Annual Research Report
  • [Journal Article] ゲノムから読み解く嗅覚の進化2015

    • Author(s)
      新村芳人
    • Journal Title

      アロマリサーチ

      Volume: 16 Pages: 164-171

    • Related Report
      2015 Annual Research Report
  • [Journal Article] 嗅覚受容体遺伝子の進化2015

    • Author(s)
      新村芳人
    • Journal Title

      におい・かおり環境学会誌

      Volume: 46 Pages: 261-263

    • NAID

      130007602873

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals.2014

    • Author(s)
      Niimura Y, Matsui A, Touhara K
    • Journal Title

      Genome Research

      Volume: 24 Issue: 9 Pages: 1485-1496

    • DOI

      10.1101/gr.169532.113

    • NAID

      120006348465

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] アフリカゾウは巨大な嗅覚受容体遺伝子ファミリーをもつ ─13種有胎盤類を用いたオーソロガス遺伝子グループの比較進化解析─2014

    • Author(s)
      新村芳人
    • Journal Title

      アロマリサーチ

      Volume: 15 Pages: 366-368

    • NAID

      40020280504

    • Related Report
      2014 Research-status Report
  • [Journal Article] 嗅覚受容体遺伝子と匂い知覚の多様性2014

    • Author(s)
      新村芳人
    • Journal Title

      実験医学

      Volume: 32 Pages: 2898-2904

    • Related Report
      2014 Research-status Report
  • [Journal Article] ゲノムから読み解く嗅覚の進化2014

    • Author(s)
      新村芳人
    • Journal Title

      現代化学

      Volume: 522 Pages: 38-39

    • Related Report
      2014 Research-status Report
  • [Journal Article] The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.2013

    • Author(s)
      Wang, Z., Pascual-Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., Li, C., White, S., Xiong, Z., Fang, D., et al.
    • Journal Title

      Nature genetics

      Volume: 45 Issue: 6 Pages: 701-706

    • DOI

      10.1038/ng.2615

    • Related Report
      2013 Research-status Report 2012 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of chemosensory receptor genes from vertebrate genomes.2013

    • Author(s)
      Niimura Y
    • Journal Title

      Methods Mol. Biol.

      Volume: 1068 Pages: 95-105

    • DOI

      10.1007/978-1-62703-619-1_7

    • ISBN
      9781627036184, 9781627036191
    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Identification of olfactory receptor genes from mammalian genome sequences.2013

    • Author(s)
      Niimura Y.
    • Journal Title

      Methods Mol Biol

      Volume: 1003 Pages: 39-49

    • DOI

      10.1007/978-1-62703-377-0_3

    • ISBN
      9781627033763, 9781627033770
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Methodical Microarray Design Enables Surveying of Expression of a Broader Range of Genes in Ciona intestinalis2013

    • Author(s)
      Matsumae H, et al.
    • Journal Title

      Gene

      Volume: 519 Issue: 1 Pages: 82-90

    • DOI

      10.1016/j.gene.2013.01.042

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics.2012

    • Author(s)
      Yoshihito Niimura
    • Journal Title

      Current Genomics

      Volume: 13 Pages: 103-114

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] hzAnalyzer : Detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets2011

    • Author(s)
      T.A.Johnson, Y.Niimura, H.Tanaka, Y.Nakamura, T.Tsunoda
    • Journal Title

      Genome Biology

      Volume: 12 Issue: 3

    • DOI

      10.1186/gb-2011-12-3-r21

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Dynamic evolution of olfactory receptor genes in mammals2016

    • Author(s)
      Yoshihito Niimura
    • Organizer
      Germany & Japan Workshop on Evolutionary Genomics
    • Place of Presentation
      国立遺伝学研究所(静岡県三島市)
    • Year and Date
      2016-03-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ムスク香を感知する嗅覚受容体の匂い応答性と進化2015

    • Author(s)
      佐藤成見、白須未香、新村芳人、伊原さよ子、東原和成
    • Organizer
      日本味と匂学会第49回大会
    • Place of Presentation
      じゅうろくプラザ(岐阜県岐阜市)
    • Year and Date
      2015-09-25
    • Related Report
      2015 Annual Research Report
  • [Presentation] ゲノム、進化、嗅覚:7億年にわたる嗅覚受容体遺伝子進化の物語2015

    • Author(s)
      新村芳人
    • Organizer
      日本味と匂学会第49回大会
    • Place of Presentation
      じゅうろくプラザ(岐阜県岐阜市)
    • Year and Date
      2015-09-25
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Evolution of olfactory receptor genes in primates and other mammals2015

    • Author(s)
      Yoshihito Niimura
    • Organizer
      第17回日本進化学会大会
    • Place of Presentation
      中央大学後楽園キャンパス(東京都文京区)
    • Year and Date
      2015-08-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 嗅覚の多様性と進化 ~哺乳類から植物まで~2015

    • Author(s)
      新村芳人
    • Organizer
      第17回日本進化学会大会
    • Place of Presentation
      中央大学後楽園キャンパス(東京都文京区)
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] Expansion and contraction of the olfactory receptor gene universe in mammals: –Superior sense of smell in African elephants?2015

    • Author(s)
      Yoshihito Niimura
    • Organizer
      The 4th International Seminar on Biodiversity and Evolution
    • Place of Presentation
      京都大学野生動物研究センター(京都府京都市)
    • Year and Date
      2015-06-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structure-activity relationship and evolution of musk odor receptors in mammals2015

    • Author(s)
      Narumi Sato, Mika Shirasu, Aya Kato-Namba, Keiichi Yoshikawa, Yoshihito Niimura, Sayoko Ihara, Kazushige Touhara
    • Organizer
      AChemS 2015 Annual Meeting
    • Place of Presentation
      Bonita Springs, Florida (USA)
    • Year and Date
      2015-04-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ゲノムから読み解く嗅覚の進化2014

    • Author(s)
      新村芳人
    • Organizer
      アロマ・サイエンス・フォーラム2014
    • Place of Presentation
      東京
    • Year and Date
      2014-12-12
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] ヒト官能評価とマウス嗅球応答を指標にした嗅覚受容体アンタゴニストによる悪臭制御の評価2014

    • Author(s)
      加藤 (難波) 綾、堀尾奈央、新村芳人、吉川敬一、齋藤菜穂子、中村純二、東原和成
    • Organizer
      日本味と匂学会第48回大会
    • Place of Presentation
      静岡
    • Year and Date
      2014-10-02
    • Related Report
      2014 Research-status Report
  • [Presentation] Expansion and contraction of the olfactory receptor universe: Orthology among 13 placental mammals highlights the evolutionary fate of genes2014

    • Author(s)
      Yoshihito Niimura
    • Organizer
      Annual Meeting of the Society for Molecular Biology and Evolution 2014
    • Place of Presentation
      サンファン(プエルトリコ)
    • Year and Date
      2014-06-06
    • Related Report
      2014 Research-status Report
  • [Presentation] Expansion and contraction of the olfactory receptor universe: Orthology among 13 placental mammals highlights the evolutionary fate of genes2014

    • Author(s)
      Yoshihito Niimura, Atsushi Matsui, Kazushige Touhara
    • Organizer
      第14回東京大学生命科学シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2014-04-26
    • Related Report
      2014 Research-status Report
  • [Presentation] 環境センサーとしての嗅覚受容体の進化~比較ゲノムの視点から~2013

    • Author(s)
      新村芳人
    • Organizer
      第82回日本寄生虫学会大会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes2012

    • Author(s)
      Takeshi Hase and Yoshihito Niimura*
    • Organizer
      Society for Molecular Biology and Evolution Annual Meeting
    • Place of Presentation
      Dublin, Ireland
    • Related Report
      2012 Research-status Report
  • [Presentation] Expression analysis in neural tissues of the Chordate, Ciona intestinalis by the use of a customized microarray2012

    • Author(s)
      Hiromi Matsumae*, Mayuko Hamada, Manabu Fujie, Hiroshi Tanaka, Yoshihito Niimura, Takeshi Kawashima
    • Organizer
      Society for Molecular Biology and Evolution Annual Meeting
    • Place of Presentation
      Dublin, Ireland
    • Related Report
      2012 Research-status Report
  • [Presentation] 哺乳類における霊長類の嗅覚受容体遺伝子レパートリーの進化2012

    • Author(s)
      松井淳*、新村芳人
    • Organizer
      第28回日本霊長類学会大会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Exomeデータを利用した霊長類の嗅覚受容体遺伝子の比較解析2012

    • Author(s)
      松井淳*、郷康広、豊田敦、会津智幸、石崎比奈子、今井啓雄、藤山秋佐夫、平井啓久、新村芳人
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] Diversity of Olfactory Receptor Gene Repertoires among 38 Mammals2011

    • Author(s)
      Niimura Y, Matsui A
    • Organizer
      Annual Meeting of the Society for Molecular Biology and Evolution
    • Place of Presentation
      京都
    • Related Report
      2011 Research-status Report
  • [Presentation] Comparative evolutionary analyses of olfactory receptor gene repertoires among five primates and eight non-primate mammals2011

    • Author(s)
      Matsui A, Niimura Y
    • Organizer
      The 5th International Symposium of the Biodiversity and Evolution Global COE project "Evolutionary Consequences of Biological Interactions -genome to ecosystem-"
    • Place of Presentation
      京都
    • Related Report
      2011 Research-status Report
  • [Presentation] 霊長類の嗅覚受容体遺伝子のレパートリーは少ないのか?2011

    • Author(s)
      松井淳、新村芳人
    • Organizer
      日本進化学会第13回大会
    • Place of Presentation
      京都
    • Related Report
      2011 Research-status Report
  • [Presentation] Difference in gene duplicability causes the difference in overall structure of protein-protein interaction networks among eukaryotes2011

    • Author(s)
      Hase T, Tanaka H, Niimura Y
    • Organizer
      Young Researchers Conference on Evolutionary Genomics
    • Place of Presentation
      東京
    • Related Report
      2011 Research-status Report
  • [Presentation] 匂いの遺伝学2011

    • Author(s)
      新村芳人
    • Organizer
      東京医科歯科大学難治疾患研究所市民公開講座―最先端生命科学講座シリーズ 第2回―(招待講演)
    • Place of Presentation
      東京
    • Related Report
      2011 Research-status Report
  • [Presentation] Expansion and contraction of the olfactory receptor universe: What determines the fate of genes?

    • Author(s)
      Yoshihito Niimura
    • Organizer
      NIG Workshop: Evolution of Junk DNAs
    • Place of Presentation
      三島(国立遺伝学研究所)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 哺乳類進化における嗅覚受容体遺伝子ファミリーの膨張と収縮:13種の真獣類を用いた比較解析

    • Author(s)
      新村芳人、松井淳、東原和成
    • Organizer
      日本味と匂学会第47回大会
    • Place of Presentation
      仙台
    • Related Report
      2013 Research-status Report
  • [Presentation] 哺乳類進化における嗅覚受容体遺伝子ファミリーの膨張と収縮:13種の真獣類を用いた比較解析

    • Author(s)
      新村芳人、松井淳、東原和成
    • Organizer
      日本遺伝学会第85回大会
    • Place of Presentation
      慶應義塾大学 日吉キャンパス
    • Related Report
      2013 Research-status Report
  • [Presentation] Evolution of olfactory receptor gene repertoires in primates

    • Author(s)
      松井淳、新村芳人、東原和成
    • Organizer
      The 11th International Symposium on Molecular and Neural Mechanisms of Taste and Olfactory Perception
    • Place of Presentation
      九州大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 遺伝子とゲノムで探る化学感覚の進化

    • Author(s)
      新村芳人
    • Organizer
      第6回 香りと味に関する産学フォーラム
    • Place of Presentation
      東京大学本郷キャンパス
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Evolution of olfactory receptor genes in vertebrates- Interaction between genomes and environments

    • Author(s)
      Yoshihito Niimura
    • Organizer
      1st International Conference on Nano-Bio-Medicine Convergence (NBMC-2014)
    • Place of Presentation
      釜山
    • Related Report
      2013 Research-status Report
    • Invited
  • [Book] Chemosensory Transduction2016

    • Author(s)
      Touhara K, Niimura Y, Ihara S
    • Total Pages
      409
    • Publisher
      Academic Press
    • Related Report
      2015 Annual Research Report
  • [Book] Olfactory Receptor Genes: Evolution. in Encyclopedia of Life Sciences2014

    • Author(s)
      Yoshihito Niimura
    • Total Pages
      12
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2014 Research-status Report
  • [Book] 進化学事典2013

    • Author(s)
      新村芳人
    • Total Pages
      4
    • Publisher
      共立出版
    • Related Report
      2012 Research-status Report
  • [Book] 興奮する匂い 食欲をそそる匂い ~遺伝子が解き明かす匂いの最前線~2012

    • Author(s)
      新村芳人
    • Total Pages
      304
    • Publisher
      技術評論社
    • Related Report
      2011 Research-status Report
  • [Book] Evolution of chemosensory receptor genes in primates and other mammals., Post-Genome Biology of Primates (eds. Hirohisa Hirai, Hiroo Imai, Yasuhiro Go)2012

    • Author(s)
      Yoshihito Niimura
    • Total Pages
      20
    • Publisher
      Springer
    • Related Report
      2011 Research-status Report
  • [Book] Protein-protein interaction networks: Structures, evolution, and application to drug design. Protein Interaction / Book 2 (ed. Weibo Cai)2012

    • Author(s)
      Takeshi Hase, Yoshihito Niimura
    • Total Pages
      22
    • Publisher
      InTech
    • Related Report
      2011 Research-status Report
  • [Book] 嗅覚受容体遺伝子ファミリー『化学受容の科学』(東原和成 編)2012

    • Author(s)
      新村芳人
    • Total Pages
      16
    • Publisher
      化学同人
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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