In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018.

In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Research Abstract Details 

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In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Abstract Text:

Hiroyuki Ichida,Kazuyuki Maeda,Hisashi Ichise,Tomoki Matsuyama,Tomoko Abe,Katsuyoshi Yoneyama,Takato Koba,Hiroyuki Ichida,Kazuyuki Maeda,Hisashi Ichise,Tomoki Matsuyama,Tomoko Abe,Katsuyoshi Yoneyama,Takato Koba,Hiroyuki Ichida,Kazuyuki Maeda,Hisashi Ichise,Tomoki Matsuyama,Tomoko Abe,Katsuyoshi Yoneyama,Takato Koba,

We have developed a restriction landmark genome scanning (RLGS) system in silico, involving two-dimensional electrophoretic analysis of DNA by computer simulation that is based on the availability of whole-genome sequences for specific organisms. We applied the technique to the analysis of the Xanthomonas oryzae pathovar oryzae (Xoo) MAFF 311018, which causes bacterial blight in rice. The coverage that was found to be achievable using RLGS in silico, as a percentage of the genomic regions that could be detected, ranged from 44.5% to 72.7% per image. However, this reached a value of 96.7% using four images that were obtained with different combinations of landmark restriction enzymes. Interestingly, the signal intensity of some of the specific spots obtained was significantly lower than that of other surrounding spots when MboI, which cleaves unmethylated 5'-GATC-3' sites, was used. DNA gel blot analysis with both DNA adenine methylase (Dam)-sensitive and -insensitive isoschizomers (MboI and Sau3AI) revealed that Dam-mediated DNA adenine methylation had indeed occurred at these particular sites. These results suggest that a significant portion of the 5'-GATC-3' sites within the Xoo genome is stably methylated by Dam.

In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Publishing Authors By Initials

H Ichida,K Maeda,H Ichise,T Matsuyama,T Abe,K Yoneyama,T Koba,H Ichida,K Maeda,H Ichise,T Matsuyama,T Abe,K Yoneyama,T Koba,H Ichida,K Maeda,H Ichise,T Matsuyama,T Abe,K Yoneyama,T Koba,

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In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Biochemical and biophysical research communication

VOLUME: 363

Page Numbers: 852-6

Journal Abbreviation: Biochem. Biophys. Res. Commun.

ISSN: 0006-291X

DAY: 24

MONTH: 09

YEAR: 2007

In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Information

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LANGUAGE: eng

NlmUniqueID: 372516

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Grant and Affiliation Information for In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018.

AFFILIATION: Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271-8510, Japan. ichida@riken.jp

Country: United States

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MEDLINETA: Biochem Biophys Res Commun

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