Fig. 3

Sub-telomeric multigene family expansions in Plasmodium vinckei parasites. a Violin plots show sub-telomeric multigene family size variations among RMPs and Plasmodium falciparum. The erythrocyte membrane antigen 1 and fam-c multigene families are expanded in the non-Katangan P. vinckei parasites (red). Apart from these families, multigene families have expanded in P. vinckei similar to that in Plasmodium chabaudi. The Katangan isolate PvvCY (purple) has a smaller number of family members compared to non-Katangan isolates (orange) except for lysophospholipases, p235 and pir gene families. b Maximum Likelihood phylogeny of 99 ema1 (top) and 328 fam-c (bottom) genes in RMPs. Branch nodes with good bootstrap support (> 70) are marked in red. The first coloured band denotes the RMP species to which the particular gene taxon belongs to. The heatmap denotes the relative gene expression among rings, trophozoite, schizont and gametocyte stages in the RMPs for which data are publicly available. Orange denotes high relative gene expression and white denotes low relative gene expression, while grey denotes lack of information. Gene expression was classified into three categories based on FPKM level distribution—High (black) denotes the top 25% of ranked FPKM of all expressed genes (FPKM > 256), Low (light grey) is the lower 25% of all expressed genes (FPKM < 32) and Medium level expression (grey; 32 < FPKM< 256). “P” denotes pseudogenes. Four vinckei-group (P. chabaudi and P. vinckei subspecies)-specific clades (clades I–IV; orange), two vinckei-specific clade (clades IV and V; purple) and one non-Katangan-specific clade (clade VI; blue) can be identified within ema1 family with strong gene expression, maximal during ring stages. Rest of the family’s expansion within non-Katangan P. vinckei isolates are mainly pseudogenes with weak transcriptional evidence. The fam-c gene phylogeny shows the presence of four distinctly distal clades (A) with robust basal support (96–100). Of the four clades, two are pan-RMP (grey) and two are vinckei-group-specific (orange), each consisting of fam-c genes positionally conserved across the member subspecies. Most members of these clades show medium to high gene expression during asexual blood stages. Other well-supported clades can be classified as either berghei-group-specific (two; green), vinckei-group-specific (two; orange), P. vinckei-specific (two; purple) or non-Katangan P. vinckei-specific clades (three; blue). There is evidence of significant species-specific expansion with striking examples in Plasmodium yoelii (i), P. chabaudi (ii) and in P. v. brucechwatti (iii)