Multi-species comparative genomics: synteny and genome rearrangements

Comparative analysis of closely related genomes is expected to yield significant insights into the processes of evolution, development, and regulation. The recently sequenced genomes of twelve fruit fly (genus Drosophila ) species and other insects provide an ideal data set for this purpose. The primary focus of this research effort is on computational analysis of genome synteny (analysis of relative gene-order conservation between species), chromosomal dynamics, and genome rearrangement between species. We have developed computational methods to process draft genome assemblies and to infer cross-species synteny. Additionally, we have developed computationally efficient algorithms to infer evolutionary rearrangement event counts and ancestral synteny blocks with the ability to handle a large set of species with high gene counts. Finally, we analyzed chromosomal rearrangements due to large-scale events such as multi-gene inversions, and fine-scale events such as single-gene relocation. Our work provides new methodologies to enable fast comparative analysis of multi-species genome-scale datasets. Our results open a window into evolutionary chromosomal reorganization within a set of eukaryotic species and highlight the role of large-scale and fine-scale rearrangement events.