Fig. 2

Structural variations and genotypic diversity among Plasmodium vinckei parasites. a Chromosomal rearrangements in P. vinckei parasites. Pairwise synteny was assessed between the five P. vinckei subspecies and Plasmodium berghei (to represent the earliest common RMP ancestor). The 14 chromosomes of different RMP genomes are arranged as a Circos plot and the ribbons (grey) between them denote regions of synteny. Three reciprocal translocation events (red) and one inversion (blue) accompany the separation of the different P. vinckei subspecies. A pan-vinckei reciprocal translocation between chromosomes VIII and X was observed between P. vinckei and other RMP genomes. Within the P. vinckei subspecies, two reciprocal translocations, between chromosomes V and XIII, and between chromosomes V and VI, separate Plasmodium vinckei petteri and P. v. baforti from the other three subspecies. A small inversion of ∼100 kb region in chromosome 14 has occurred in PvvCY alone. b Maximum likelihood phylogeny of different RMP species with high-quality reference genomes based on protein alignment of 3920 one-to-one orthologs (bootstrap values of each node are shown). Genomes of three human malaria species—Plasmodium falciparum, Plasmodium vivax and Plasmodium knowlesi—were included in the analysis as outgroups. c Maximum likelihood phylogenetic tree of all sequenced RMP isolates based on 1,010,956 high-quality SNPs (bootstrap values of each node are shown). There exists significant genotypic diversity among the P. vinckei isolates compared to the other RMPs. All P. vinckei subspecies have begun to diverge from their common ancestor well before subspeciation events within Plasmodium yoelii and Plasmodium chabaudi. Genetic diversity within P. v. petteri and P. v. baforti isolates are similar to those observed within P. yoelii and P. chabaudi isolates while P. v. lentum and P. v. brucechwatti isolates have exceptionally high and low divergences respectively. Genes with significantly high Ka/Ks ratios in different subspecies-wise comparisons (as indicated by connector lines), the gene’s Ka/Ks ratio averaged across all indicated P. vinckei comparisons and geographical origin of the isolates are shown