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The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria

Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across...

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Autores principales: Lavi, Bar, Levy Karin, Eli, Pupko, Tal, Hazkani-Covo, Einat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941160/
https://www.ncbi.nlm.nih.gov/pubmed/29608719
http://dx.doi.org/10.1093/gbe/evy044
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author Lavi, Bar
Levy Karin, Eli
Pupko, Tal
Hazkani-Covo, Einat
author_facet Lavi, Bar
Levy Karin, Eli
Pupko, Tal
Hazkani-Covo, Einat
author_sort Lavi, Bar
collection PubMed
description Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across 20 proteobacterial strains. We first identified IRs in Escherichia coli K-12 substr MG1655 and showed that they are overabundant. We next aimed to test whether this overabundance is reflected in the conservation of IRs over evolutionary time scales. To this end, for each perfect IR identified in E. coli MG1655, we collected orthologous sequences from related proteobacterial genomes. We next quantified the evolutionary conservation of these IRs, that is, the presence of the exact same IR across orthologous regions. We observed high conservation of perfect IRs: out of the 234 examined orthologous regions, 145 were more conserved than expected, which is statistically significant even after correcting for multiple testing. Our results together with previous experimental findings support a model in which imperfect IRs are corrected to perfect IRs in a preferential manner via a template switching mechanism.
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spelling pubmed-59411602018-05-15 The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria Lavi, Bar Levy Karin, Eli Pupko, Tal Hazkani-Covo, Einat Genome Biol Evol Research Article Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across 20 proteobacterial strains. We first identified IRs in Escherichia coli K-12 substr MG1655 and showed that they are overabundant. We next aimed to test whether this overabundance is reflected in the conservation of IRs over evolutionary time scales. To this end, for each perfect IR identified in E. coli MG1655, we collected orthologous sequences from related proteobacterial genomes. We next quantified the evolutionary conservation of these IRs, that is, the presence of the exact same IR across orthologous regions. We observed high conservation of perfect IRs: out of the 234 examined orthologous regions, 145 were more conserved than expected, which is statistically significant even after correcting for multiple testing. Our results together with previous experimental findings support a model in which imperfect IRs are corrected to perfect IRs in a preferential manner via a template switching mechanism. Oxford University Press 2018-02-22 /pmc/articles/PMC5941160/ /pubmed/29608719 http://dx.doi.org/10.1093/gbe/evy044 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Lavi, Bar
Levy Karin, Eli
Pupko, Tal
Hazkani-Covo, Einat
The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title_full The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title_fullStr The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title_full_unstemmed The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title_short The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
title_sort prevalence and evolutionary conservation of inverted repeats in proteobacteria
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941160/
https://www.ncbi.nlm.nih.gov/pubmed/29608719
http://dx.doi.org/10.1093/gbe/evy044
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