Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)

With genomic data (generated by classical, functional, structural, proteo- and other `omic' approaches) accumulating at a stupendous rate, there is an ever increasing need for the development of new, more efficient and more sensitive computational methods. To highlight aspects of our computational needs, we will present results that emerged from the comparative genome analysis of mitochondria. Having originated from an alpha-proteobacterial endosymbiont, these eukaryotic organelles contain small and extremely variable genomes, and are thus perfect model systems for the much more complex eubacterial and archaeal genomes. We are currently in vestigating mitochondrial DNAs (mtDNAs) in a lineage of unicellular, primitive protistan eukaryotes, the jakobids, with the aim to understand the evolution of mitochondrial genomes, genes and their regulation. Because these organisms are difficult to grow, biochemical approaches aimed at understanding gene regulation are laborious, thus it is possible to capitalize considerably from predictions on genome and gene organization, and regulatory elements. Contrary to approaches in which molecular data (gene order, sequence similarities) are used to infer the phylogenetic relationships among a group of organism, we know their phylogeny and employ this information to identify and model more or less conserved genetic elements and structural RNA genes that are difficult to spot by conventional methods, in a phylogenetic-comparative approach.