(A) Ribosome footprint (green) and mRNA (blue) profiles of the ring-infected erythrocyte surface antigen 2, RESA2 pseudogene (PF11_0512) in rings (R) and merozoites (M). Both, the annotated isoform from PlasmoDB version 7.1 and the gene model for the alternate isoform inferred using ribosome profiling and W2 genomic DNA sequencing data from this study is depicted (CDS, white boxes; HMM-defined UTRs, black lines). The red star indicates a homopolymeric tract in which a single base deletion causes a premature stop codon (red triangle), which coincides with the site of ribosome drop off. (B) Ribosome footprint and mRNA profiles of erythrocyte vesicle protein 1, EVP1 (PFD0495c). This gene is transcribed in all stages yet translational efficiencies are relatively low, as evidenced by a depletion of ribosomes on the CDS of the gene particularly in early trophozoites (log2TE = −2.6, −2.9, −1.0, −2.1, −1.4 in rings, early trophozoites, late trophozoites, schizonts, and merozoites, respectively). (CDS, white boxes; HMM-defined UTRs, black lines. Mappability = mappability score at that position; range 0 (white) to 30 (black). rM = coverage (reads per million reads mapped).