Comparative Analysis of Genomic Rearrangements in Microorganisms

The theoretical genome rearrangement problem (sorting a permutation by transpositions and inversions) has attracted a good deal of attention from mathematicians and computer scientists, and comparative genome sequence data from closely related microbial strains and species are now accumulating at a rapid pace. Detailed inspection of this data will help us understand the evolutionary forces that determine genomic structures and stabilities in microbial systems. Important questions concern the extent to which microbial trees contain inconsistent branches caused by horizontal transfer events of individual genes. With the advent of completely sequenced data from closely related genomes, we expect many previously unknown properties of genome rearrangements to be uncovered, opening new questions for mathematicians and biologists alike. The whole genome sequences of two chlamydian parasites, Chlamydia trachomatis and Chlamydia pneumoniae, have recently been published [1, 3, 4]. Chlamydia are obligate intra-cellular parasites, responsible for a variety of diseases in non-human mammals and birds, but also frequently transmitted to humans. For example, C. trachomatis is the causative agent of trachoma, a major cause of blindness in Asia and Africa and C. pneumoniae causes pneumonia and bronchitis. A comparative analysis of rearrangement events in the two genomes has revealed a large proportion of transpositions and inversions of segments of very small length, consisting of just one or two genes. This phenomenon calls for modified methods for estimating the number of different rearrangement events. In this project we have modified the Derange II computer program of Blanchette et al. [2]. We then use a simulation technique for determining appropriate parameters.