Asexual Populations of the Human Malaria Parasite, Plasmodium falciparum, Use a Two-Step Genomic Strategy to Acquire Accurate, Beneficial DNA Amplifications
Figure 2
Genes within DHODH amplicons from round 1 clones.
A. Mid-density microarray results of round 1 clone C (other clones, Fig. S1) showing a 70 kb amplicon at the beginning of chromosome 6 (DHODH amplicon). B. Gene coverage (spotted microarray) of the DHODH amplicon (D (blue); C (green); E (red); F (magenta). Average log2 ratios are calculated from 3 experimental replicates over 1–3 probes per gene. There were no other significant amplifications detected anywhere in the genome (significance cut off >1.5 fold change, FDR <10%). Gene numbers 1–25 correspond to those listed in Table S7. C. Summary of DHODH amplicon size (both spotted and mid-density microarrays). The DHODH target gene (no. 19) is depicted in red, A/T tracks at amplicon junctions are indicated by a grey circle (black outline, shared junction; red outline, junction within introns). The amplicon boundaries of each clone were verified using qPCR (Fig. S8). D. Confirmation of DHODH copy number by qPCR. Front and rear primers (Table S12) were used to detect the DHODH gene. Values are relative to Dd2 (grey) and normalized against seryl t-RNA synthetase (PF07_0073) copy number. Error bars depict standard error. Significance was determined against Dd2 (*, p value<0.05 and **, p value<0.005).