Comprehensive Analysis of Complex Copy Number Variations in the Plasmodium falciparum Genome via Long-Read Sequencing: Implications for Antimalarial Resistance and Broad Genomic Insights

Abstract Introduction/Objective The genome of Plasmodium falciparum, characterized by a high AT content and a propensity for copy number variations (CNVs), presents a model for understanding how genomes adapt to stress. Our research focused on the prevalence and distribution of CNVs highlights long-read sequencing as a tool for detecting complex structural variants in other models. Methods/Case Report P. falciparum parasites were cultured and treated with DSM1 and aphidicolin that induce replication stress. Long-read sequencing was conducted using the Oxford Nanopore Technology Minion, with an emphasis on an optimizing DNA extraction method for preserving intact chromosomes. Visualization of CNVs, including tandem and inverted duplications, was achieved through a custom R Shiny application that allowed both quantitative and qualitative assessments. Results (if a Case Study enter NA) Long read sequencing identified an enrichment of multiple CNV types in treated samples, with a significant enrichment of inverted duplications as well as other types of structural variants. Aphidicolin and DSM1-treated samples demonstrated significant accumulation of these variations compared to controls (2.0 and 5.6-fold, respectively with a p value of < 0.0001 in both treatment groups). These occurred mainly in core genomic regions that do not contain variable gene copies. An increase in the number of inverted duplications may be related to stress response to the treatment and may be a potential adaptive mechanism of the parasite. Our manual single-read visualization technique made it possible to visualize the structure of various CNV types, which provides unique insight on CNVs as they arise in single genomes. Conclusion We hypothesize that inverted duplications represent stalled replication forks, and we are currently assessing their frequency in replicating and non-replicating cells. This study highlights the role of long-read sequencing in detecting complex genomic structures in P. falciparum, which may influence the parasite’s resistance to drug treatment. These findings not only advance our understanding of malaria pathology but also aid our comprehension of how cancer cells might react to drug-induced stress and the mechanisms behind CNV formation in neoplastic cells.