The generation of extra-chromosomal DNA amplicons in antimalarial resistant Plasmodium falciparum

Extra-chromosomal(ec) DNAs are genetic elements that exist separately from the genome. Since ecDNA can carry beneficial genes, they are a powerful adaptive mechanism in cancers and many pathogens. For the first time, we report ecDNA contributing to antimalarial resistance in Plasmodium falciparum, the most virulent human malaria parasite. Using pulse field gel electrophoresis combined with copy number analysis, we detected two ecDNA elements that differ in structure and migration. Treatment with structure-specific nucleases revealed that one ecDNA is likely linear fragments of another large, complex ecDNA molecule. Using deep sequencing, we show that ecDNA originates from the chromosome and expansion of an ecDNA-specific sequence may improve its segregation. We speculate that ecDNA is maintained using established mechanisms due to shared characteristics with the mitochondrial genome. Implications of ecDNA discovery in this organism are wide-reaching due to the potential for new strategies to target resistance development.