FIG. 5.

SERA loci across the Plasmodium and Theileria genera. HMM hits for the protease and C-terminal SERA domains are indicated schematically on the contigs on which they were found. Breaks in species tracks indicate discontinuities at contig ends. Where they exist, gene annotations have been indicated. When HMM matches existed on multiple short contigs in a species, the contigs were ordered according to orthology relationships with related species inferred from the phylogeny. SERA genes that have been successfully knocked out in P. falciparum are marked in red, while those refractory to deletion are in black. Where orthology is clearly discernible from the phylogeny, it is marked by vertical blocks that join species. Orthologies of P. gallinaceum and T. annulata genes are ambiguous due to a postspecies duplication. This ambiguity is represented by a bifurcation in the orthology block. The phylogeny of Cys SERA genes indicates a duplication of SERA8 present only in P. gallinaceum as well as a duplication resulting in SERA6 and SERA7 in Plasmodium spp. (excluding P. gallinaceum). Ambiguities arising from these duplications are represented by bifurcations in the orthology blocks. Where it is clearly present, the orthology of flanking sequence is also noted. Protease domains marked in green do not contain active-site mutations, whereas protease domains marked in blue contain the cysteine-to-serine active-site mutation. The presence of secondary-site mutations has been marked below the corresponding protease domain. RT-PCR expression levels (this study) and protein abundance as a percentages of SERA5 are shown above the P. falciparum (3D7) track (16, 17). Similarly, relative copy number expression measurements for P. vivax as a percentage of P. vivax SERA4 are shown above the P. vivax track (22). KO, knockout.