GRSR: A tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Abstract

Background: Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and translocations etc. Many algorithms for calculating rearrangement scenarios between two genomes have been proposed. Very often, the calculated rearrangement scenario is not unique for the same pair of permutations. Hence, how to decide which calculated rearrangement scenario is more biologically meaningful becomes an essential task. Up to now, several mechanisms for genome rearrangements have been studied. One important theory is that genome rearrangement may be mediated by repeats, especially for reversal events. Many reversal regions are found to be flanked by a pair of inverted repeats. As a result, whether there are repeats at the breakpoints of the calculated rearrangement events can shed a light on deciding whether the calculated rearrangement events is biologically meaningful. To our knowledge, there is no tool which can automatically identify rearrangement events and check whether there exist repeats at the breakpoints of each calculated rearrangement event. Results: In this paper, we describe a new tool named GRSR which allows us to compare multiple unichromosomal genomes to identify "independent" (obvious) rearrangement events such as reversals, (inverted) block interchanges and (inverted) transpositions and automatically searches for repeats at the breakpoints of each rearrangement event. We apply our tool on the complete genomes of 28 Mycobacterium tuberculosis strains and 24 Shewanella strains respectively. In both Mycobacterium tuberculosis and Shewanella strains, our tool finds many reversal regions flanked by a pair of inverted repeats. In particular, the GRSR tool also finds an inverted transposition and an inverted block interchange in Shewanella, where the repeats at the ends of rearrangement regions remain unchanged after the rearrangement event. To our knowledge, this is the first time such a phenomenon for inverted transposition and inverted block interchange is reported in Shewanella. Conclusions: From the calculated results, there are many examples supporting the theory that the existence of repeats at the breakpoints of a rearrangement event can make the sequences at the breakpoints remain unchanged before and after the rearrangement events, suggesting that the conservation of ends could possibly be a popular phenomenon in many types of genome rearrangement events.