| Recent progress in genome-scale sequencing and comparative mapping raises new challenges in studies of genome rearrangements. Although the pairwise genome rearrangement problem is well studied, algorithms for reconstructing the most parsimonious rearrangement scenarios for multiple species are in great demand. The previous approaches to the multiple genome rearrangement problem were largely based on the breakpoint distance rather than on a more biologically accurate rearrangement (reversal) distance. Another shortcoming of the existing software tools is their inability to analyze rearrangements (inversions, translocations, fusions, and fissions) of multichromosomal genomes.; This thesis proposes a new multiple genome rearrangement algorithm that is based on the rearrangement (rather than breakpoint) distance and that is applicable to both unichromosomal and multichromosomal genomes. We further apply this algorithm for genome-scale phylogenetic tree reconstruction and deriving ancestral gene orders. In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and putative rearrangement scenarios for the human, cat, cow and mouse genomes. In this thesis, we also offer a new lead for the integration of comparative mapping data in genome rearrangement studies. Finally, we describe the web version of the algorithm, which has recently been made available for phylogenetic tree reconstruction and for the exploration of the rearrangement scenarios. |
