Mechanisms and genomic features of copy number variation in malaria parasites

Antimalarial resistance is a major obstacle in the eradication of the malaria parasite, Plasmodium. Genome amplifications are a type of DNA copy number variation (CNV) that facilitate the overexpression of drug targets and contribute to overall parasite survival. It had previously been found that long monomeric A/T tracks are found at the breakpoints of many resistance-conferring CNVs but other features that contribute to their formation were not known. By adapting a whole genome sequence analysis pipeline to investigate previously reported CNVs, we identified CNV breakpoints in parasites with near single base-pair resolution. We also found that especially stable DNA secondary structures, such as hairpins, were predicted to form near five shared CNV breakpoints which demonstrates that the initiating event for their formation likely occurred at these sites. Furthermore, we determined that long monomeric A/T tracts were enriched within Plasmodium genomes regardless of their overall genome A/T content and that they were frequently the CNV breakpoint for all species. Further in-depth analyses of whole genome sequencing data sets detected signatures of error-prone repair pathways at the breakpoints and identified CNV heterogeneity. Through this work, we identified an evolutionarily conserved “trigger site” model of CNV formation that utilizes two genomic features to first form the initial lesion (hairpins) and facilitate microhomology-mediated repair (A/T tracks) across the highly repetitive Plasmodium genomes. Our findings reinforce the need for further investigation of the molecular mechanisms of CNV creation utilized by Plasmodium species.