Figure 3: Analysis of expanded or positively selected gene families in T. gondii.

(a) Analysis of positive selective pressure among T. gondii gene families based on d_N/d_S. Red values indicate categories with significantly elevated d_N/d_S ratios, indicating positive selection for diversification, while blue values indicate categories with significantly reduced values, indicative of selection for conservation. Analysis based on 16 reference T. gondii genomes, although similar patterns were also seen for all 62 strains. Horizontal black line d_N/d_S median; yellow square, d_N/d_S mean; mean values significantly different than the category ‘Other’ (P≤0.05, Mann–Whitney–Wilcoxon test) are denoted with ‘*’. (b) Heatmap of the abundance of SPDs in conserved orthogroups. The number of genes in orthogroups containing SPD genes was determined across the 16 T. gondii reference genomes, H. hammondi and N. caninum, and plotted as a heatmap. Each row is an orthogroup, and the colour of each cell represents the number of genes in that orthogroup, range 0–19. (c) Schematic representation of domain structure of T. gondii protein families A to E. Family names and average protein lengths per family are indicated on the right. HVR, hypervariable region; KRDEGST-rich domain, protein domain rich in polar amino acids Lysine (K), Arginine (R), Aspartate (D), Glutamate (E), Serine (S), Threonine (T) and Glycine (G); SP, signal peptide; TMM, transmembrane domain; TR, tandem-repeat domain; VR, protein domain of variable length and sequence. Sequence motifs for each tandem-repeat unit are depicted in Logo format. Extra (ED) and intracellular (ID) protein domains, as predicted by Phobius, are indicated below protein schemes. (d) Life-cycle expression of TgFAM genes. Heatmap of log₂-normalized microarray expression values for TgFAM genes across the T. gondii life cycle^36,66,67. Background values for the array are near log₂ of 5. Samples for unsporulated oocysts (Day 0 Oocyst), sporulated oocysts (Day 10 Oocyst), intermediate host tachyzoites (Day 2 Tachy), intermediate host dormant bradyzoite cysts (Day 8 Brady), and enteric stage merozoites (Day 5 Mero) are plotted.