Development Of Population Genomics Data For The Protist Theileria parva, An Intracellular Pathogen Of Cattle

East Coast fever is an acute fatal disease of cattle caused by the tick-transmitted intracellular pathogen Theileria parva. The stakeholder and research communities have identified the development of an effective recombinant vaccine a high priority. In the last few years reverse vaccinology, based on whole genome annotation and population genomics data, has emerged as a primary approach to identify putative vaccine antigens from genome sequence data. The application of reverse vaccinology to T. parva presents several fundamental challenges, starting with the isolation of parasite DNA for genome sequencing without sacrificing the bovine host. We describe the use of DNA sequence capture approaches to isolate T. parva genomic DNA from T. parva-infected bovine lymphocyte cell lines. We successfully captured T. parva sequence reads that map to >98% of the reference genome. When assembled, the reads produce high quality de novo draft genome assemblies also corresponding to >98% of the reference genome. We have now obtained similar results with the genome capture of different isolates, including that of the distant strain T. parva lawrencei. This approach will facilitate the generation of population genomics resources necessary for reverse vaccinology of T. parva, incuding the identification of allelic variants, genotyping markers and the generation of the SNP data necessary for population structure studies. These results are directly applicable to a variety of intracellular pathogens, including other apicomplexans.