The apicomplexans are a phylum of protozoan parasites that contribute significantly to eukaryotic morbidity and mortality. As apicomplexans are phylogenetically set apart from other species, knowledge cannot be easily transferred to apicomplexans from classical model organisms. Knowledge of apicomplexan transcriptional regulation, in particular, remains elusive. In this thesis, comparative genomics approaches are utilized to identify and characterize transcriptional networks in Plasmodia and other apicomplexans.

We implemented a conservation-based transcription factor binding site discovery approach to better understand transcriptional regulation in two newly sequenced Plasmodium genomes. Binding sites were found to be conserved in both core processes like catabolism and more parasite-specific ones like invasion. The conservation patterns of discovered binding sites suggest a link between sites and parasite phenotypic differences.

The genetic bases of phenotypic differences can be understood, in part, by investigating constraints on three aspects of transcriptional networks—transcription factors, regulatory sequences and gene expression. To this end, we explored evolutionary constraints on Plasmodium sequence and expression via existing and novel approaches. We found that transcription factors have relatively less constrained coding regions than genes involved in processes like metabolism. This is consistent with the view that transcription factors and associated networks are diverging to support phenotypic differences. Transcription factors and genes important to the parasites lifestyle have conserved upstream regions suggestive of complex transcriptional control. Additionally, a cross-species expression comparison revealed that Plasmodium-specific genes, many of which are lifestyle genes, exhibit more expression divergence than less phyletically-restricted genes. This suggests that transcriptional networks involving these genes are modified to support disparate parasite lifestyles.

To obtain a phylum-wide view of network divergence, we assessed conservation patterns of three experimentally verified Plasmodium transcription factor binding sites in eleven apicomplexans. None of the associated networks were conserved in ail species but two networks were conserved across disparate phylogenetic orders of apicomplexans. Combining the conservation analysis with discoveries from a study of transcription factor orthology patterns highlights two modes of network evolution in these parasites: (i) evolution of disparate transcription factors and (ii) rewiring of common binding sites and their factors to regulate disparate processes in different species.