Document Detail


Significant deviations in the configurations of homologous tandem repeats in prokaryotic genomes.
MedLine Citation:
PMID:  20172489     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Shintaro Hirayama; Satoshi Mizuta
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Genomics, proteomics & bioinformatics     Volume:  7     ISSN:  2210-3244     ISO Abbreviation:  Genomics Proteomics Bioinformatics     Publication Date:  2009 Dec 
Date Detail:
Created Date:  2010-02-22     Completed Date:  2010-06-03     Revised Date:  2013-04-17    
Medline Journal Info:
Nlm Unique ID:  101197608     Medline TA:  Genomics Proteomics Bioinformatics     Country:  China    
Other Details:
Languages:  eng     Pagination:  163-74     Citation Subset:  IM    
Copyright Information:
Copyright 2009 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.
Affiliation:
Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.
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MeSH Terms
Descriptor/Qualifier:
Chromosomes
Gene Duplication*
Genome, Archaeal*
Genome, Bacterial*
Genome, Fungal*
Genomics
Prokaryotic Cells*
Tandem Repeat Sequences / genetics*

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