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Analysis of gene expression network of natural and artificial allotetraploids using next generation sequencers

Research Project

Project/Area Number 22687021
Research Category

Grant-in-Aid for Young Scientists (A)

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

Principal Investigator

OSADA Naoki  国立遺伝学研究所, 集団遺伝研究系, 助教 (70416270)

Project Period (FY) 2010-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥21,840,000 (Direct Cost: ¥16,800,000、Indirect Cost: ¥5,040,000)
Fiscal Year 2013: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2012: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2011: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2010: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Keywordsゲノム / 異質倍数体 / トランスクリプトーム / ゲノム進化 / 遺伝子発現 / 進化 / 植物
Research Abstract

Understanding the interaction between two different genomes is important issue in evolutionary biology research, especially when the two genomes were incorporated into the same organisms. I analyzed the genomic and expression properties of recently established natural allotetraploid plants, of which parental species are relative to the model species Arabidopsis thaliana. Using massively parallel sequencers, genome sequences of parental species and transcriptome data of allotetraploid species were studied.

Report

(5 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (47 results)

All 2014 2013 2012 2011 2010 Other

All Journal Article (20 results) (of which Peer Reviewed: 20 results,  Open Access: 2 results) Presentation (23 results) (of which Invited: 1 results) Book (4 results)

  • [Journal Article] Extracting population genetics information from a diploid genome sequence (review)2014

    • Author(s)
      Naoki Osada
    • Journal Title

      Front. Ecol. Evol

      Volume: 2 Pages: 7-7

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Whole genome sequencing of Tibetan macaque (Macaca thibetana) provides new insight into the macaque evolutionary history2014

    • Author(s)
      Zhenxin Fan, Guang Zhao, Peng Li, Naoki Osada, Jinchuan Xing, Yong Yi, Lianming Du, Pedro Silva, Hongxing Wang, Ryuichi Sakate, Xiuyue Zhang, Huailiang Xu, Bisong Yue*, Jing Li
    • Journal Title

      Mol. Biol. Evol.

      Volume: online advance Issue: 6 Pages: 1475-1489

    • DOI

      10.1093/molbev/msu104

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [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
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis : male-driven evolution, demography, and natural selection2013

    • Author(s)
      Naoki Osada
    • Journal Title

      Genetics

      Volume: 195 Issue: 3 Pages: 1007-1025

    • DOI

      10.1534/genetics.113.156703

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Weak selection and protein evolution (review)2012

    • Author(s)
      Hiroshi Akashi, Naoki Osada, Tomoko Ohta
    • Journal Title

      Genetics

      Volume: 192 Issue: 1 Pages: 15-31

    • DOI

      10.1534/genetics.112.140178

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)2012

    • Author(s)
      Chi-Chun Huan, Kuo-Hsiang Hung, Wei-KuangWang, Chao-Li Huang, Tsai-Wen Hsu, Naoki Osada, Chi-Chuan Hwang, Tzen-Yuh Chiang
    • Journal Title

      Gene

      Volume: 499 Issue: 1 Pages: 194-201

    • DOI

      10.1016/j.gene.2012.02.037

    • Related Report
      2013 Final Research Report 2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Footprints of natural and artificial selection for photoperiod pathway genes in Oryza2012

    • Author(s)
      Chao-Li Huang, Cheng-Yu Hung, Yu-Chung Chiang, Chi-Chuan Hwang, Tsai-Wen Hsu, Chi-Chun Huang, Kuo-Hsiang Hung, Kun-Chan Tsai, Kuo-HsiungWang, Naoki Osada, Barbara Anna Schaal, Tzen-Yuh Chiang
    • Journal Title

      Plant J

      Volume: 70 Issue: 5 Pages: 769-782

    • DOI

      10.1111/j.1365-313x.2012.04915.x

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mitochondrial-nuclear interactions and accelerated compensatory evolution : Evidence from the primate cytochrome c oxidase complex2012

    • Author(s)
      Naoki Osada, Hiroshi Akashi
    • Journal Title

      Mol. Biol. Evol

      Volume: 29 Issue: 1 Pages: 337-346

    • DOI

      10.1093/molbev/msr211

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chao-Li Huang et al. Footprints of natural and artificial selection for photoperiod pathway genes in Oryza2012

    • Author(s)
      Chao-Li Huang et al.
    • Journal Title

      The Plant Journal

      Volume: 70 Pages: 769-782

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome2012

    • Author(s)
      Atsunori Higashino et al.
    • Journal Title

      Genome Biology

      Volume: 13

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Weak selection and protein evolution2012

    • Author(s)
      Hiroshi Akashi et al.
    • Journal Title

      Genetics

      Volume: 192 Pages: 15-31

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Population genetics in non-model organisms : II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms2011

    • Author(s)
      Renchao Zhou, Shaoping Ling, Wenming Zhao, Naoki Osada, Sufang Chen, Meng Zhang, Hua Bao, Cairong Zhong, Bing Zhang, Xuemei Lu, David Turissini, Norman C. Duke, Jian Lu, Suhua Shi, Chung-I Wu
    • Journal Title

      Mol Biol Evol

      Volume: 28 Issue: 10 Pages: 2833-2842

    • DOI

      10.1093/molbev/msr102

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Phylogenetic inconsistency caused by ancient sex-biased migration2011

    • Author(s)
      Naoki Osada
    • Journal Title

      PLoS ONE

      Volume: 6 Issue: 9 Pages: e25549-e25549

    • DOI

      10.1371/journal.pone.0025549

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A22011

    • Author(s)
      Uno, Y., Osada, N.
    • Journal Title

      BMC Evol.Biol.

      Volume: 11 Issue: 1 Pages: 283-283

    • DOI

      10.1186/1471-2148-11-283

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phylogenetic inconsistency caused by ancient sex-biased migration2011

    • Author(s)
      Osada, N.
    • Journal Title

      PloS ONE

      Volume: 6

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of MHC class I transcripts of a Malaysian cynomolgus macaque by high throughput pyrosequencing and EST libraries2011

    • Author(s)
      Aarnink, et al
    • Journal Title

      Immunogenetics

      Volume: 63 Issue: 11 Pages: 703-713

    • DOI

      10.1007/s00251-011-0550-8

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel DNA sequence isolated from blood donors with high transaminase levels2011

    • Author(s)
      Sato, et al
    • Journal Title

      Hepatol.Res.

      Volume: 41 Issue: 10 Pages: 971-981

    • DOI

      10.1111/j.1872-034x.2011.00848.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Population genetics in non-model organisms : II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms2011

    • Author(s)
      Zhou, et al
    • Journal Title

      Mol.Biol.Evol.

      Volume: 28 Pages: 2833-2842

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A family tree of vertebrate chemokine receptors for a unified nomenclature2011

    • Author(s)
      Nomiyama, et al
    • Journal Title

      Dev.Comp.Immunol.

      Volume: 35 Pages: 705-715

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multi-locus analysis of genetic divergence between outcrossing Arabidopsis species : evidence of genome-wide admixture2010

    • Author(s)
      Wei-KuangWang, Chuan-Wen Ho, Kuo-Hsiang Hung, Kuo-HsiungWang, Chi-Chun Huang, Hitoshi Araki, Chi-Chuan Hwang, Naoki Osada, Tzen-Yuh Chiang
    • Journal Title

      New Phytol

      Volume: 188 Issue: 2 Pages: 488-500

    • DOI

      10.1111/j.1469-8137.2010.03383.x

    • Related Report
      2013 Final Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster2013

    • Author(s)
      Naoki Osada
    • Organizer
      ISEGB2013
    • Place of Presentation
      Chung-Hsing University, Taichung, Taiwan
    • Year and Date
      2013-11-08
    • Related Report
      2013 Final Research Report
  • [Presentation] キイロショウジョウバエにおける集団内でのcis およびtrans 遺伝子発現変異の定量2013

    • Author(s)
      長田直樹, 宮城竜太郎, 高橋文
    • Organizer
      日本遺伝学会
    • Place of Presentation
      慶応大学日吉キャンパス
    • Year and Date
      2013-09-20
    • Related Report
      2013 Final Research Report
  • [Presentation] Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis2013

    • Author(s)
      Naoki Osada, Shigeki Nakagome, Shuhei Mano, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    • Organizer
      SMBE2013
    • Place of Presentation
      Chicago, USA
    • Related Report
      2013 Final Research Report
  • [Presentation] 霊長類のゲノム進化2013

    • Author(s)
      長田直樹
    • Organizer
      日本人類学会
    • Place of Presentation
      国立科学博物館筑波研究施設
    • Related Report
      2013 Annual Research Report
  • [Presentation] 51. キイロショウジョウバエにおける集団内でのcisおよびtrans遺伝子発現変異の定量2013

    • Author(s)
      長田直樹,宮城竜太郎,高橋文
    • Organizer
      日本遺伝学会
    • Place of Presentation
      慶應大学日吉キャンパス
    • Related Report
      2013 Annual Research Report
  • [Presentation] Compensatory Evolution between Mitochondrial and Nuclear Genomes2012

    • Author(s)
      Osada, N.
    • Organizer
      The 8^<th> Okazaki Biological Conference
    • Place of Presentation
      基礎生物学研究所(岡崎市)
    • Year and Date
      2012-03-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] Inferring natural selection by stratifying a single genome sequence2012

    • Author(s)
      Naoki Osada
    • Organizer
      SMBE2012
    • Place of Presentation
      Dublin, Ireland
    • Related Report
      2013 Final Research Report
  • [Presentation] 多座位データを用いたゲノムヒストリーの推定2011

    • Author(s)
      長田直樹
    • Organizer
      統計数理研究所共同利用研究集会
    • Place of Presentation
      統計数理研究所(立川市)
    • Year and Date
      2011-12-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] Inference of population history using a single genome data2011

    • Author(s)
      Osada, N.
    • Organizer
      日本分子生物学会,第34回大会
    • Place of Presentation
      パシフィコ横浜(横浜市)
    • Year and Date
      2011-12-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] Genetic diversity and population history of macaque monkeys2011

    • Author(s)
      Osada, N.
    • Organizer
      Genomic Conservation and Diversity of Organisms : Beyond the NGS time of Life Science
    • Place of Presentation
      Tainan, Taiwan
    • Year and Date
      2011-12-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] メタゲノム解析とその応用2011

    • Author(s)
      長田直樹
    • Organizer
      メタゲノム解析を利用した下水道情報網基盤構築に関する研究集会
    • Place of Presentation
      諏訪市
    • Year and Date
      2011-11-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] 機能喪失とCpG サイトの崩壊による旧世界ザルCYP1A2 遺伝子の高い遺伝的多様性2011

    • Author(s)
      長田直樹, 宇野泰広
    • Organizer
      第83回日本遺伝学会
    • Place of Presentation
      京都大学
    • Year and Date
      2011-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] 機能喪失とCpGサイトの崩壊による旧世界ザルCYP1A2遺伝子の高い遺伝的多様性2011

    • Author(s)
      長田直樹, 宇野泰広
    • Organizer
      日本遺伝学会,第83回大会
    • Place of Presentation
      京都大学(京都市)
    • Year and Date
      2011-09-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Compensatory evolution between mitochondrial and nuclear genomes : evidence from primate respiratory chain complex genes2011

    • Author(s)
      Naoki Osada, Hiroshi Akashi
    • Organizer
      SMBE2011
    • Place of Presentation
      Kyoto, Japan
    • Year and Date
      2011-07-28
    • Related Report
      2013 Final Research Report
  • [Presentation] Compensatory evolution between mitochondrial and nuclear genomes : evidence from primate respiratory chain complex genes2011

    • Author(s)
      Osada, N., Akashi, H.
    • Organizer
      SMBE2011
    • Place of Presentation
      京都大学(京都市)
    • Year and Date
      2011-07-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] 霊長類の中のヒト:ゲノム多様性の種間比較2011

    • Author(s)
      長田直樹
    • Organizer
      遺伝研共同研究集会:ヒト形質のゲノム発掘による新しい進化人類学の創成
    • Place of Presentation
      国立遺伝学研究所(三島市)
    • Year and Date
      2011-07-01
    • Related Report
      2011 Annual Research Report
  • [Presentation] Inference of population history using a single genome data2011

    • Author(s)
      Naoki Osada
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2013 Final Research Report
  • [Presentation] ミトコンドリア・核遺伝子間の弱有害補完モデル : 霊長類COX 遺伝子群の進化を例に2010

    • Author(s)
      長田直樹, 明石裕
    • Organizer
      第90回日本遺伝学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2010-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] ミトコンドリア・核遺伝子間の弱有害補完モデル:霊長類COX遺伝子群の進化を例に2010

    • Author(s)
      長田直樹, 明石裕
    • Organizer
      第90回日本遺伝学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Population Genetics of Non-human Primates : How AreWe Diverse?2010

    • Author(s)
      Naoki Osada
    • Organizer
      International Primatological Society Congress
    • Place of Presentation
      Kyoto, Japan
    • Year and Date
      2010-09-13
    • Related Report
      2013 Final Research Report
  • [Presentation] Population Genetics of Non-human Primates : How Are We Diverse?2010

    • Author(s)
      Naoki Osada
    • Organizer
      International Primatoiogical Society Congress
    • Place of Presentation
      京都大学
    • Year and Date
      2010-09-13
    • Related Report
      2010 Annual Research Report
  • [Presentation] マルチローカスデータを用いた進化生態学研究について2010

    • Author(s)
      長田直樹
    • Organizer
      第12回日本進化学会
    • Place of Presentation
      東京工業大学
    • Year and Date
      2010-08-04
    • Related Report
      2010 Annual Research Report
  • [Presentation] 霊長類でのX染色体と常染色体との遺伝的多様性の比について

    • Author(s)
      長田直樹
    • Organizer
      日本人類学会
    • Place of Presentation
      慶応大学日吉キャンパス
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] ヒトは病気とともに進化した2013

    • Author(s)
      太田博樹,長谷川眞理子,長田直樹,大橋順,中込滋樹,間野修平,西野穣,長岡朋人,柴田弘紀
    • Total Pages
      232
    • Publisher
      勁草書房
    • Related Report
      2013 Annual Research Report
  • [Book] An overview of transcriptome studies in nonhuman primates. In: Post genome Biology of primates2012

    • Author(s)
      Naoki Osada
    • Total Pages
      286
    • Publisher
      Springer
    • Related Report
      2012 Annual Research Report
  • [Book] An overview of transcriptome studies in nonhuman primates. In : Post genome Biology of primates (Primatology monographs)2012

    • Author(s)
      Naoki Osada
    • Publisher
      Springer-Verlag
    • Related Report
      2011 Annual Research Report
  • [Book] Bucentaur (Bcnt) Gene Family : Gene Duplication and Retrotransposon Insertion In Gene Duplication2011

    • Author(s)
      Iwashita, S., Osada, N.
    • Publisher
      InTech
    • Related Report
      2011 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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