The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting in a higher rate of C→T transition. Intraoperon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas interoperon intergenic regions are usually devoid of transcription. Hence these two types of intergenic regions (IGRs) can be compared to find out the contribution of replication-associated mutations (RAM) and transcription-associated mutations (TrAM) towards bringing variation in genomes. In our work, we performed a polymorphism spectra comparison between intraoperon IGRs and interoperon IGRs in genomes of two well-known closely related bacteria such as Escherichia coli and Salmonella enterica. In general, the size of intraoperon IGRs was smaller than that of interoperon IGRs in E. coli and S. enterica. Interestingly, the polymorphism frequency at intraoperon IGRs was 2.5-fold lesser than that in the interoperon IGRs in E. coli genome. Similarly, the polymorphism frequency at intraoperon IGRs was 2.8-fold lesser than that in the inter-operon IGRs in S. enterica genome. Therefore, the intraoperon IGRs were often observed to be more conserved. In the case of interoperon IGRs, the T→C transition frequency was a minimum of two times more frequent than T→A transversion frequency whereas in the case of intraoperon IGRs, T→C transition frequency was similar to that of T→A transversion frequency. The polymorphism was purine-biased and keto-biased more in intraoperon IGRs than the inter-operon IGRs. In E. coli, the transition/transversion ratio was observed as 1.639 and 1.338 in inter-operon and in intraoperon IGRs, respectively. In S. enterica, the transition/transversion ratio was observed as 2.134 and 2.780 in inter-operon and in intraoperon IGRs, respectively. The observation in this study indicates that transcribable IGRs might not always have higher polymorphism frequency than nontranscribable IGRs. The lower polymorphism frequency at intraoperon IGRs might be attributed to different events such as the transcription-coupled DNA repair, sequences facilitating translation initiation and avoidance of Rho-dependent transcription termination.

在复制和转录过程中，基因组中单链区域的临时暴露使得该区域易受胞嘧啶脱氨作用的影响，从而导致更高的 C→T 转换率。操纵子内基因间区域与操纵子中相邻的共转录基因一起进行转录，而操纵子间基因间区域通常没有转录。因此，可以比较这两种类型的基因间区域 (IGR)，以找出复制相关突变 (RAM) 和转录相关突变 (TrAM) 对基因组变异的贡献。在我们的工作中，我们对两种众所周知的密切相关细菌（如大肠杆菌和肠沙门氏菌。一般而言，在大肠杆菌和肠道链球菌中，操纵子内 IGRs 的大小小于操纵子间 IGRs 的大小。有趣的是，在大肠杆菌基因组中，操纵子内 IGR 的多态性频率比操纵子间 IGR 的多态性频率低 2.5 倍。类似地，intraoperon IGRs 的多态性频率比S. enterica中操纵子间 IGRs 的多态性频率低 2.8 倍基因组。因此，通常观察到操纵子内 IGR 更保守。在操纵子间 IGRs 的情况下，T→C 转换频率至少是 T→A 转换频率的两倍，而在 intraoperon IGRs 的情况下，T→C 转换频率与 T→A 转换频率相似. 多态性在操纵子内 IGR 中比在操纵子间 IGR 中更偏向于嘌呤和偏向于酮。在大肠杆菌中，在操纵子间和操纵子内 IGR 中观察到的转换/颠换比分别为 1.639 和 1.338。在S. enterica 中，在操纵子间和操纵子内 IGR 中观察到的转换/颠换比分别为 2.134 和 2.780。本研究中的观察表明，可转录的 IGR 可能并不总是比不可转录的 IGR 具有更高的多态性频率。intraoperon IGR 的较低多态性频率可能归因于不同的事件，例如转录偶联 DNA 修复、促进翻译起始的序列和避免 Rho 依赖性转录终止。