In this project , A comparative genomic analysis was carried out to identify and detect unique differences between the two species, using publicly available P. vivax Illumina and PacBio sequencing data and new P. simium sequences (from LSHTM). The analysis involved multiple sequence alignments (MSA) and construction of phylogenetic trees. In addition to a global population structure analysis, a set of 13 erythrocytic invasion genes significant to the pathogenesis of malaria were compared. The results reveal that no unique genomic variants (e.g. SNPs or InDels) between the species. Clustering was not observed according to geographic region, and although some grouping was observed in some genes ,it lacked in consistency. Further research is necessary before arriving at a definite answer of whether the P. simium is a separate new zoonotic species or a P. vivax derived but my project suggests the latter.
You can find codes for how this comparative genome analysis was carried out in the main branch!