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Motivation: Genome rearrangement plays an important role in evolutionarybiology and has profound impacts on phenotype in organisms ranging frommicrobes to humans. The mechanisms for genome rearrangement events remainunclear. Lots of comparisons have been conducted among different species. Toreveal the mechanisms for rearrangement events, comparison of differentindividuals/strains within the same species or genus (pan-genomes) is morehelpful since they are much closer to each other. Results: We study themechanism for inversion events via core-genome scaffold comparison of differentstrains within the same species. We focus on two kinds of bacteria, Pseudomonasaeruginosa and Escherichia coli, and investigate the inversion events amongdifferent strains of the same specie. We find an interesting phenomenon thatlong (larger than 10,000 bp) inversion regions are flanked by a pair ofInverted Repeats (IRs) (with lengths ranging from 385 bp to 27476 bp) which areoften Insertion Sequences (ISs).This mechanism can also explain why thebreakpoint reuses for inversion events happen. We study the prevalence of thephenomenon and find that it is a major mechanism for inversions. The otherobservation is that for different rearrangement events such as transpositionand inverted block interchange, the two ends of the swapped regions are alsoassociated with repeats so that after the rearrangement operations the two endsof the swapped regions remain unchanged. To our knowledge, this is the firsttime such a phenomenon is reported for transposition event.

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