Significant Deviations in the Configurations of Homologous Tandem Repeats in Prokaryotic Genomes

Abstract

We explored the possibilities of whole-genome duplication (WGD) in prokaryotic species, where we performed statistical analyses of the configurations of the central angles between homologous tandem repeats (TRs) on the circular chromosomes. At first, we detected TRs on their chromosomes and identified equivalent tandem repeat pairs (ETRPs); here, an ETRP is defined as a pair of tandem repeats sequentially similar to each other. Then we carried out statistical analyses of the central angle distributions of the detected ETRPs on each circular chromosome by way of comparisons between the detected distributions and those generated by null models. In the analyses, we estimated a P value by a simulation using the Kullback–Leibler divergence as a distance measure between two distributions. As a result, the central angle distributions for 8 out of the 203 prokaryotic species showed statistically significant deviations (P<0.05). In particular, we found out the characteristic feature of one round of WGD in Photorhabdus luminescens genome and that of two rounds of WGD in Escherichia coli K12.

Ail and PagC-Related Proteins in the Entomopathogenic Bacteria of Photorhabdus Genus

“…Interestingly, another gene encoding an outer membrane protein, the ompF -like gene, probably underwent a tandem duplication [62] . Characteristic features of an ancient whole-genome duplication were also detected in the P. luminescens TT01 genome [63] . In addition, a 275-kilobase single block duplication, with cryptic phenotypic consequences, was observed in phenotypic variants of P. luminescens [64] .…”