Development of a method for core genome identification as a basis for microbial comparative genomics

2010 Fiscal Year Final Research Report

• Project/Area Number: 20310125
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: ゲノム情報科学
• Research Institution: National Institute for Basic Biology
• Principal Investigator: UCHIYAMA Ikuo National Institute for Basic Biology, ゲノム情報研究室, 助教 (90243089)
• Project Period (FY): 2008 – 2010
• Keywords: ゲノム / 進化 / 微生物

Research Abstract

As a fundamental basis for comparative analysis of microbial genomes that have undergone complex evolutionary processes including horizontal gene transfers, we have investigated a method to identify a "genomic core structure" among related genomes that is mainly inherited through vertical transfers. Our method is based on extracting the regions that have conserved gene order among the related genomes. We applied our method to various genomic data to test its validity and established a system to accumulate the resulting core structures of the published data into a database. We also developed a tool that implements the protocol for core genome analysis including visualization of core structures, and applied it to actual comparative studies of closely related microbial genomes.

Research Products

• [Journal Article] BMC Microbiology (2011)
  • Author(s): Kawai M., Furuta Y., Yahara K., Tsuru T., Oshima K., Handa N., Takahashi N., Yoshida M., Azuma T., Hattori M., Uchiyama I., Kobayashi I.
  • Journal Title: 11 104
  • Peer Reviewed
• [Journal Article] Birth and death of genes linked to chromosomal inversion, Proc. (2011)
  • Author(s): Furuta Y., Kawai M., Yahara K., Takahashi N., Handa N., Tsuru T., Oshima K., Yoshida M., Azuma T., Hattori M., Uchiyama I., Kobayashi I.
  • Journal Title: Natl.Acad.Sci.USA 108 Pages: 1501-1506
  • Peer Reviewed
• [Journal Article] MBGD update 2010 : toward a comprehensive resource for exploring microbial genome diversity (2010)
  • Author(s): Uchiyama I., Higuchi T., Kawai M.
  • Journal Title: Nucleic Acids, Res. 38 Pages: D361-D365
  • Peer Reviewed
• [Journal Article] Complete Genome Sequence of Macrococcus caseolyticus Strain JSCS5402 Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci (2009)
  • Author(s): Baba T., Kuwahara-Arai K., Uchiyama I., Takeuchi F., Ito T., Hiramatsu K.
  • Journal Title: J.Bacteriol. 191 Pages: 1180-1190
  • Peer Reviewed
• [Journal Article] Multiple genome alignment for identifying the core structure among moderately related microbial genomes (2008)
  • Author(s): 内山郁夫
  • Journal Title: BMC Genomics 9 Pages: 515
  • Peer Reviewed
• [Presentation] RECOG : a framework for systematic approaches to microbial genome comparison (2011)
  • Author(s): 内山郁夫
  • Organizer: International Symposium on Omics Approach to Microbes
  • Place of Presentation: NEERI, Nagpur, India
  • Year and Date: 20110217-20110218
• [Presentation] Systematic approach for large-scale microbial comparative genomics (2009)
  • Author(s): 内山郁夫
  • Organizer: The 4^<th> Global COE International Symposium 2009 joint with the 19^<th> Hot Spring Harbor Symposium Molecular Evolution and Bioinformatics
  • Place of Presentation: 九州大学,福岡
  • Year and Date: 20091101-20091102
• [Presentation] 大規模比較ゲノム解析の推進に向けて:比較ゲノムワークベンチRECOGの開発と、ピロリ菌東アジア株ゲノム解析への応用 (2009)
  • Author(s): 内山郁夫
  • Organizer: 第11回日本進化学会大会
  • Place of Presentation: 北海道大学,札幌
  • Year and Date: 20090902-20090904
• [Presentation] CoreAligner : Multiple genome alignment for identifying the genomic core among moderately related microbial genomes (2008)
  • Author(s): 内山郁夫
  • Organizer: 19th International Conference on Genome Informatics
  • Place of Presentation: Marriot Surfers Paradise, Gold Coast, Australia
  • Year and Date: 2008-12-01
• [Presentation] ゲノム進化過程の解明に向けた近縁細菌ゲノムのインフォマティクス (2008)
  • Author(s): 内山郁夫
  • Organizer: 第10回日本進化学会大会
  • Place of Presentation: 東京大学駒場キャンパス
  • Year and Date: 2008-08-24
• [Book] メタゲノム解析技術の最前線(服部正平監修)(比較ゲノムにおけるバイオインフォマティクス基盤) (2011)
  • Author(s): 内山郁夫
  • Total Pages: 54-65
  • Publisher: CMC出版
• [Book] Omics approaches to protein function prediction(Daisuke Kihara ed.)(Functional inference in microbial genomics based on large-sccale comparative analysis) (2011)
  • Author(s): 内山郁夫
  • Publisher: Springer
• [Remarks] ホームページ等
• [Remarks] 微生物比較ゲノムデータベースMBGD
  • URL: http://mbgd.genome.ad.jp
• [Remarks] CoreAligner プログラム
  • URL: http://mbgd.genome.ad.jp/CoreAligner