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.
Bibliographical noteFunding Information:
E.L.K. is a fellow of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. T.P. is supported by the Israel Science Foundation grant 802/16. E.H.C. was supported by the Israel Cancer Association grant 20150038 and by the Open University of Israel Research fund.
© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
- Inverted repeats
- Palindrome conservation
- Palindrome evolution
- Template switching