Theileria infections in African cattle and buffalo: understanding genetic variation and speciation

Abstract

East Coast fever, caused by the apicomplexan parasite Theileria parva, has an estimated annual death toll of over a million cattle in endemic sub-Saharan regions. The African Cape buffalo is the natural reservoir of T. parva and rarely exhibits clinical symptoms when infected, but transmits the parasite to cattle via a tick vector. Previous studies based on a few genetic markers showed that buffalo-derived T. parva subpopulations contain greater antigenic diversity than those from cattle. Interestingly, cattle are infected and killed by T. parva of buffalo origin, but cannot transmit those parasites, suggesting that a degree of host specificity exists. The characterization of genetic variation within and between cattle- and buffalo-derived T. parva is critical to understand the molecular mechanism(s) of host specificity. To overcome obstacles in T. parva biology that prevent the straightforward acquisition of sufficient DNA for whole genome sequencing (WGS), we adapted a DNA capture approach to select T. parva from a mix of parasite and bovine DNA obtained from T. parva-infected bovine lymphocyte cultures. To gain access to variable genomic regions that cannot be characterized through read mapping approaches, we assembled the captured reads de novo. From starting material of <1%-4% parasite DNA in a mixed sample from host and parasite, >98% of sequence reads post-capture are of parasite origin and >97% of the genome is recovered, reflecting the method’s high specificity and sensitivity. We used this whole genome DNA capture followed by sequencing to generate WGS data from 15 cattle- and 24 buffalo-derived T. parva isolates. This resulted in the generation of the first assembly of a buffalo-derived T. parva isolate. Furthermore, we determined that cattle- and buffalo-derived T. parva isolates differ in various measures at levels consistent with speciation. Finally, capture and analysis of members of the T. parva repeat (Tpr) multigene family, which encode some of the most variable antigen families in the species, enabled the study of Tpr evolution and initial inferences of its possible involvement in parasite-host interactions. These results have greatly advanced the study of the T. parva genome and improved our understanding of the evolution of this parasite population.