In silico identification and characterization of stress and virulence associated repeats in Salmonella

Gourab Das; Surojit Das; Shanta Dutta; Indira Ghosh

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In silico identification and characterization of stress and virulence associated repeats in Salmonella

机译：在Silico鉴定和表征沙门氏菌中的应激和毒力

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Abstract So much genomic similarities yet causing different diseases, is like a paradox in Salmonella biology. Repeat is one of the probes that can explain such differences. Here, a comparative genomics approach is followed to identify and characterize repeats that might play role in adaptation and pathogenesis. Repeats are non-randomly distributed in the genomes except few typhoid causing strains. Perfect long repeats are rare compare to polymorphic ones and both are statistically consistent. Significant differences in repeat densities in stress related genes manifest its probable participation in survival and virulence. 573 and 1053 repeat loci have been identified which are exclusively associated with stress and virulent genes respectively. In Salmonella Typhi, an octameric VNTR locus is found in between acrD and yffB genes having more than 25 perfect copies across Salmonella Typhi but possesses only single copy in other serovars. This repeat can be used as a diagnostic probe for typhoid. Graphical abstract Display Omitted Highlights ? Repeats are non-randomly distributed in Salmonella genomes. ? Significant differences in repeat densities between stress and non-stress related genes has been observed. ? A normalized pointwise mutual information based method is developed to find stress and virulence related repeats. ? Total 1053 and 573 unique repeat loci have been detected related to virulence and stress in Salmonella .

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来源
《Genomics》 |2018年第1期|共12页
作者
Gourab Das; Surojit Das; Shanta Dutta; Indira Ghosh;
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作者单位

School of Computational and Integrative Sciences Jawaharlal Nehru University (JNU);

National Institute of Cholera and Enteric Diseases (NICED);

National Institute of Cholera and Enteric Diseases (NICED);

School of Computational and Integrative Sciences Jawaharlal Nehru University (JNU);

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原文格式 PDF
正文语种 eng
中图分类医学遗传学;
关键词
Repetitive sequences; Association; Stress; Virulence; Salmonella;

机译：重复序列;关联;压力;毒力;沙门氏菌;

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2. Molecular Analysis and Identification of Virulence Gene on pRST98 from Multi-Drug Resistant Salmonella typhi [J] . RuiHuang, ShuyanWu, XueguangZhang, 细胞与分子免疫学：英文版 . 2005,第002期
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4. Stress Physiology and Virulence Characterization of Phomopsis asparagi （Sacc.） Bub6k isolated from Asparagus in Jiangxi Province of China [J] . Yueping ZHANG, Guangyu CHEN, Shaochun LUO, 农业科学与技术（英文版） . 2012,第007期
5. In silico identification and characterization of stress and virulence associated repeats in Salmonella [J] . GourabDas, SurojitDas, ShantaDutta, Genomics . 2018,第1期

机译：沙门氏菌中压力和毒力相关重复序列的计算机鉴定和表征
6. In silico identification and characterization of stress and virulence associated repeats in Salmonella [J] . Gourab Das, Surojit Das, Shanta Dutta, Genomics . 2018,第1期

机译：在Silico鉴定和表征沙门氏菌中的应激和毒力
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In silico identification and characterization of stress and virulence associated repeats in Salmonella

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