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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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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. |
format | Online Article Text |
id | pubmed-5941160 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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