3P290 Analysis of tandem repeats found in 44 prokaryotic genomes and genome evolution

Mizuta, Satoshi; Abulimiti, Abuduaini; Kimura, Takaharu; Oosawa, Kenji; Shimizu, Tetsu

doi:10.2142/biophys.44.s262_2

Cited by 1 publication

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“…However, because the differences are systematic to some extent, the discrepancy can be understood on the assumption that a foreign body of a certain length had been inserted into E. coli K12 genome during some events in the course of the evolution of E. coli K12 after 2R WGD. Actually, in E. coli K12 genome, a dissimilar region from the rest can be recognized between 45° and 90° ( 19 ) . If the foreign region is evidently identified, further analyses of the central angle distribution of the ETRPs will reveal more explicitly the relics of WGDs in E. coli K12 genome; these studies are now being advanced.…”

Section: Resultsmentioning

confidence: 99%

“…PCC7120 and claimed that WGD is most responsible for the large genome size among some possibilities. In addition, one of us (Mizuta) and colleagues analyzed 44 prokaryotic genomes based on a different methodology from the other studies; they identified equivalent tandem repeat pairs (ETRPs) on the chromosomes and examined the central angle distributions of ETRPs ( 19 ) . They found out distinctive patterns in the distributions and suggested the existence of WGD for some species including E. coli K12.…”

Section: Introductionmentioning

confidence: 99%

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

Hirayama

Mizuta

2009

Genomics, Proteomics &Amp; Bioinformatics

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%