Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats

TL;DR

This study reveals that large inversion events in bacterial genomes are frequently flanked by inverted repeats, especially insertion sequences, indicating a prevalent mechanism for genome rearrangements within species.

Contribution

It uncovers the association between inversion breakpoints and inverted repeats, particularly insertion sequences, as a major mechanism for genome inversions in bacteria.

Findings

Long inversion regions (>10,000 bp) are flanked by inverted repeats.

Inverted repeats often are insertion sequences (ISs).

Rearrangement events involve repeats at swapped region ends.

Abstract

Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of comparisons have been conducted among different species. To reveal the mechanisms for rearrangement events, comparison of different individuals/strains within the same species or genus (pan-genomes) is more helpful since they are much closer to each other. Results: We study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. We focus on two kinds of bacteria, Pseudomonas aeruginosa and Escherichia coli, and investigate the inversion events among different strains of the same specie. We find an interesting phenomenon that long (larger than 10,000 bp) inversion regions are flanked by a pair of Inverted Repeats (IRs) (with lengths ranging from 385 bp to 27476 bp) which are often Insertion Sequences (ISs).This mechanism can also explain why the breakpoint reuses for inversion events happen. We study the prevalence of the phenomenon and find that it is a major mechanism for inversions. The other observation is that for different rearrangement events such as transposition and inverted block interchange, the two ends of the swapped regions are also associated with repeats so that after the rearrangement operations the two ends of the swapped regions remain unchanged. To our knowledge, this is the first time such a phenomenon is reported for transposition event.