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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 .
机译：摘要这么多的基因组相似之处却引起了不同的疾病，就像沙门氏菌生物学的悖论就像悖论。重复是可以解释这种差异的探针之一。这里，遵循比较基因组学方法，以识别和表征可能在适应和发病机制中发挥作用的重复。除了少量伤寒引起菌株之外，重复在基因组中是非随机分布的。完美的长重复是与多态的重复比较，两者都是统计上一致的。压力相关基因中重复密度的显着差异表现出其可能参与存活和毒力。已经鉴定了573和1053，重复基因座，其分别与应力和毒性基因完全相关。在Salmonella Typhi中，八大号VNTR基因座在Acrd和YFFB基因之间发现了超过25个完美拷贝的跨脸，但只有其他塞洛瓦的单副本。该重复可以用作伤寒的诊断探针。图形抽象显示省略了亮点？重复在沙门氏菌基因组中是非随机分布的。还已经观察到应力和非应力相关基因之间重复密度的显着差异。还开发了归一化的点互信息的方法以找到应力和毒力相关的重复。还已经检测到总共1053和573个独特的重复基因座与沙门氏菌中的毒力和压力有关。

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