Kalinina Anastasia S, Suvorikova Alexandra L, Spokoiny Vladimir G, Gelfand Mikhail S
* A. A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.
† The International Research Training Group 1792, Berlin, Germany.
J Bioinform Comput Biol. 2016 Apr;14(2):1641001. doi: 10.1142/S0219720016410018. Epub 2016 Jan 14.
Detection of recombination events in a bacterial genome is both important from the evolutionary point of view, and of practical interest. Indeed, homologous recombination (HR) plays a major role in the exchange of antigenic determinants between strains. There exist statistical methods to detect recently recombined segments in whole-genome sequences that use a high local density of substitutions as a signal of HR events with a source outside considered strains. However, it is difficult to detect the HR events within a set of strains, which represent whole species diversity, due to a low number of substitutions in recombined segments and high level of diversity of strains. Here, we analyzed HR in 20 Escherichia coli (E. coli) strains to define what fraction of segments with a high substitution rate were introduced in a genome by HR. For detection of HR, we used the segmentation, performed by the adaptive weights smoothing (AWS) algorithm. It detects sharp changes in the structure of observed data analyzing only qualitative structural information. We validated the approach on simulated data, applied it to the analysis of E. coli strains, and determined the recombination rates between phylogroups.
从进化的角度以及实际应用的角度来看，检测细菌基因组中的重组事件都非常重要。事实上，同源重组（HR）在菌株间抗原决定簇的交换中起着主要作用。存在一些统计方法可用于检测全基因组序列中最近发生重组的片段，这些方法将高局部替换密度作为与所考虑菌株之外的来源发生HR事件的信号。然而，由于重组片段中的替换数量较少且菌株的多样性水平较高，因此很难在一组代表整个物种多样性的菌株中检测到HR事件。在这里，我们分析了20株大肠杆菌（E. coli）中的HR，以确定通过HR引入基因组的高替换率片段所占的比例。为了检测HR，我们使用了由自适应权重平滑（AWS）算法执行的分割方法。它仅通过分析定性结构信息就能检测到观测数据结构中的急剧变化。我们在模拟数据上验证了该方法，并将其应用于大肠杆菌菌株的分析，同时确定了不同系统发育群之间的重组率。
