Studies on features and frequencies of recombination in bacterial evolution
| Project/Area Number |
23651183
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| Research Category |
Grant-in-Aid for Challenging Exploratory Research
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| Allocation Type | Multi-year Fund |
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| Research Field |
Genome biology
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| Research Institution | Tohoku University |
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Principal Investigator |
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| Project Period (FY) |
2011 – 2013
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| Project Status |
Completed (Fiscal Year 2013)
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| Budget Amount *help |
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2013: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
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| Keywords | recombination / ShortReadManager / illumina / リコンビネーション / k-mer / ソフトウエア / イルミナリード / ビフェニル資化能 / 協奏進化 / 次世代シーケンサー / ゲノム進化 |
|---|
| Research Abstract |
To clarify features and frequencies of bacterial recombinational events, two closely related bacterial strains were mixed and incubated in a sterile soil sample. After a long period of incubation cells were recovered on a solid medium, and subjected to illumina sequencing. The illumina sequencing reads were analyzed by developing and using a computational tool named 'ShortReadManager', which is now released at http://www.ige.tohoku.ac.jp/joho/gf/index.php, and I found no evidence that indicates recombination between the two strains.
On the other hand, mutated DNA fragment of 16S ribosomal RNA gene was inserted into a genome of a soil bacteria, in which 5 copies of rRNA gene are present. The mutated fragment was expected to be replaced by the wild-type copy. By quantitative PCR analysis, we found a evidence that suggests concerted evolution of multi gene family.
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Report
(4 results)
Research Products
(120 results)
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[Journal Article] Complete genome sequence of the thermophilic PCB degrader Geobacillus sp. JF8 (NBRC 109937)2014
Author(s)
Shintani, M., Y. Ohtsubo, K. Fukuda, A. Hosoyama, S. Ohji, A. Yamazoe, N. Fujita, Y. Nagata, M. Tsuda, T. Hatta, and K. Kimbara
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Journal Title
Genome Announcements
Volume: 2
Issue: 1
DOI
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Peer Reviewed
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[Journal Article] Complete genome sequence of a Propionibacterium acnes isolate from a sarcoidosis patient.2013
Author(s)
Minegishi K, Aikawa C, Furukawa A, Watanabe T, Nakano T, Ogura Y, Ohtsubo Y, Kurokawa K, Hayashi T, Maruyama F, Nakagawa I, Eishi Y
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Journal Title
Genome Announcement
Volume: 1
Issue: 1
Pages: 16-12
DOI
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Peer Reviewed
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[Journal Article] Genomic organization and genomic structural rearrangements of SphingobiumjaponicumUT26, an archetypal gamma- hexachlorocyclohexane- degrading bacterium2011
Author(s)
Nagata, Y., S. Natsui, R. Endo, Y. Ohtsubo, N. Ichikawa, A. Ankai, A. Oguchi, S. Fukui, N. Fujita, and M. Tsuda
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Journal Title
Enzyme and Microbial Technology
Volume: 49
Pages: 499-508
Related Report
Peer Reviewed
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[Presentation] 土壌微生物の移植メタゲノム2014
Author(s)
加藤広海, 森宙史, 丸山史人, 豊田敦, 永山浩史, 大坪嘉行, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝
Organizer
第8回日本ゲノム微生物学会年会
Place of Presentation
東京
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[Presentation] Isolation of phenol-catabolic genes by cultivation-independent functional screening from metagenome of soil artificially polluted by aromatic hydrocarbons2013
Author(s)
Hirofumi Nagayama, Tomonori Sugawara, Ryo Endo, Hiromi Kato, Yoshiyuki Ohtsubo, Yuji Nagata, Hiroshi Mori, Ken, Kurokawa, and Masataka Tsuda
Organizer
2nd Thünen Symposium on Soil Metagenomics: mining and learning from metagenomes plus workshop on bioinformatic tools for soil microbiologists
Place of Presentation
Braunschweig, Germany
Related Report
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[Presentation] Design and experimental validation of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes2013
Author(s)
Hiroshi Mori, Fumito Maruyama, Hiromi Kato, Atsushi Toyoda, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Asao Fujiyama, Masataka Tsuda, and Ken Kurokawa
Organizer
2nd Thünen Symposium on Soil Metagenomics: mining and learning from metagenomes plus workshop on bioinformatic tools for soil microbiologists
Place of Presentation
Braunschweig, Germany
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