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

作　　者：Shintaro Hirayama Satoshi Mizuta 

机构地区：[1]Graduate School of Science and Technology,Hirosaki University

出　　处：《Genomics, Proteomics & Bioinformatics》2009年第4期163-174,共12页基因组蛋白质组与生物信息学报（英文版）

摘　　要：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.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.

关 键 词：whole-genome duplication statistical analysis tandem repeat Kullback-Leibler divergence PROKARYOTE 

分 类 号：Q75[生物学—分子生物学]