The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever
or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa.
We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains
(Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains.
Comparison with the reference Muguga genome sequence revealed 34 814–121 545 single nucleotide
polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic
trees were constructed with selected informative SNPs that allowed the investigation of possible complex
recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (nonsynonymous
substitutions per non-synonymous site divided by synonymous substitutions per synonymous
site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection
were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates.
This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with
prediction of possible past recombination events, providing insight into the migration, diversification, and
evolution of this parasite species in the African continent.