The prevalence and evolutionary conservation of inverted repeats in proteobacteria

Bar Lavi, Eli Levy Karin, Tal Pupko*, Einat Hazkani-Covo

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)918-927
Number of pages10
JournalGenome Biology and Evolution
Volume10
Issue number3
DOIs
StatePublished - 1 Mar 2018

Funding

FundersFunder number
Open University of Israel Research Fund
Israel Cancer Association20150038
Israel Science Foundation802/16

    Keywords

    • Inverted repeats
    • Palindrome conservation
    • Palindrome evolution
    • Template switching

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