Comparative approaches to genome evolution in Blastocystis and Entamoeba

Abstract

Parasitism has arisen independently in numerous lineages of eukaryotes. Investigating the origins of parasitism is a core question in evolutionary biology and allows identification of parasite-specific factors that aid in diagnosis and treatment. Comparative genomic studies have often been applied within clades of parasites, which allows their ancestral state to be imagined, but cannot elucidate the processes that surrounded the emergence of parasitism. This question must be approached by comparison with a free-living out-group, to reconstruct the ancestral non-parasitic state. In this thesis, I examine free-living relatives of two intestinal protists of global importance, Blastocystis sp. and Entamoeba histolytica, to explore their evolution. A draft genome sequence for Proteromonas lacertae, the non-pathogenic sister-taxon of Blastocystis, is presented along with a transcriptome for Cafeteria roenbergensis, a free-living out-group to the Blastocystis-Proteromonas clade. Together with the published Blastocystis sp. genome sequences, the P. lacertae genome and the C. roenbergensis transcriptome were used in a comparative genomic analysis. This revealed that the Blastocystis genomes are genuinely small, compared to other Stramenopiles and that this reduction is genome-wide as well as with respect to specific cellular apparatus, such as the flagellum and other motility-associated genes, which have been totally lost from the ancestor of Blastocystis. Rather than observe the same loss of function from metabolic capability, this reduction was associated with loss of gene complexity and is indicative of genomic streamlining. This is coupled with gene family expansion of Ig-like domain-containing proteins, potentially bestowing adhesive qualities to the cell surface. A transcriptome for Mastigamoeba sp., a free-living out-group to the Entamoeba genus, is also presented. The Mastigamoeba sp. transcriptome was used in a comparative analysis of the E. histolytica genome. This analysis revealed large-scale expansion of Ras-family proteins in the ancestor of Entamoeba, which may be linked to motility and phagocytosis required for pathogenesis. Analysis of cathepsins revealed processes of genomic reduction and expansion occurring within the same gene family indicating genomic streamlining and subsequent specialisation in the parasite. I have shown how we might revisit crucial questions in evolutionary biology using the latest genome sequencing technology. By generating new genomic resources for free-living protists, this thesis exposes the mechanism by which two common intestinal parasites of humans and animals evolved. It makes substantial contribution to our understanding of the origins of parasite genomes, and of microbial biodiversity, while revealing numerous parasite-specific features that will sustain future research.