Illumina paired end sequencing of DSM1 resistant clones of Plasmodium falciparum

In malaria parasites, DNA copy number variations confer resistance to drugs and host immunity but the molecular evolutionary strategies to correctly identify and stabilize advantageous changes remain unknown. Continuous challenge of Plasmodium falciparum parasites with DSM1, a novel dihydroorotate dehydrogenase (DHODH) inhibitor, reproducibly selected for de novo amplification of 34-94 Kb genomic regions, always spanning the DHODH gene. Genome-wide analysis of resistant clones revealed a simple two-step strategy to evolutionary success: populations first randomly sampled large duplications across distant poly A/T tracks to allow few parasites to gain a resistance foothold at the DHODH locus. Subsequently, increased resistance was achieved through precise, homologous head-to-tail amplifications of the founder DHODH amplicon. This two-step mechanism allows a relatively small haploid parasite population to survive new unexpected selection pressures. Pseudo-polyploidy at the relevant locus positions the parasite for future acquisition of additional beneficial mutations.