Development of a method for core genome identification as a basis for microbial comparative genomics
| Project/Area Number |
20310125
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
ゲノム情報科学
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| Research Institution | National Institute for Basic Biology |
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Principal Investigator |
UCHIYAMA Ikuo National Institute for Basic Biology, ゲノム情報研究室, 助教 (90243089)
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| Project Period (FY) |
2008 – 2010
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| Project Status |
Completed (Fiscal Year 2010)
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| Budget Amount *help |
¥18,980,000 (Direct Cost: ¥14,600,000、Indirect Cost: ¥4,380,000)
Fiscal Year 2010: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2009: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2008: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
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| Keywords | ゲノム / 進化 / 微生物 / ゲノムアライメント / 微生物ゲノム / 水平遺伝子移動 / ゲノムデータベース / 水平遺伝子異動 / 水平潰伝子移動 |
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| 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.
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Report
(4 results)
Research Products
(30 results)
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[Journal Article] BMC Microbiology2011
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.
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Journal Title
Related Report
Peer Reviewed
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[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.
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Journal Title
Natl.Acad.Sci.USA 108
Pages: 1501-1506
Related Report
Peer Reviewed
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[Journal Article] Birth and death of genes linked to chromosomal inversion2011
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.
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Journal Title
Proc.Natl.Acad.Sci.USA
Volume: 108
Pages: 1501-1506
Related Report
Peer Reviewed
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[Journal Article] Evolution in an oncogenic bacterial species with extreme genome plasticity : Helicobacter pylori East Asian genomes2011
Author(s)
Mikihiko Kawai, Yoshikazu Furuta, Koji Yahara, Takeshi Tsuru, Kenshiro Oshima, Naofumi Handa, Noriko Takahashi, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
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Journal Title
BMC Microbiology
Volume: 11
Related Report
Peer Reviewed
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