Detection of Genetic Recombination in Immune Evasion Genes of Plasmodium falciparum
- Elizabeth Winzeler, Professor of Pediatrics, University of California San Diego
- Micah Manary, Graduate Student, University of California San Diego
Plasmodium falciparum exhibits differential expression of surface membrane antigens encoded by var genes. Genetic changes within var genes will lead to increased antigenic variability resulting in a greater ability for the parasite to evade immune responses. To detect these changes over time in a controllable environment, P. falciparum was cultured over a period of a year, after which isolates were sub-cloned and submitted for paired-end whole genome sequencing. From our sequence alignments we noticed that a large number of sequencing fragments in particular regions had their mated reads aligning to two different chromosomes, corresponding to a deletion on one chromosome and a paired amplification on the other. This is consistent with a genetic recombination (gene conversion) event. To validate these findings, we designed primers that would theoretically bind to the sequence from each of the two original chromosomes involved in the recombination and thus generate a Polymerase Chain Reaction (PCR) product that spanned over the deletion/amplification event. PCR was used to amplify these regions, and the products were sent for Sanger sequencing. These new sequences were aligned with the 3D7 reference genome for P. falciparum. Our results showed that there was indeed strong evidence of recombination events at many of the locations initially suspected. These results have major implications for how P. falciparum produces antigenic variability and thus evades a consistent immune response. We are continuing to characterize these recombinations, especially to deduce the mechanism by which they may occur, with special attention being paid to how these recombinations are affecting putative vaccine targets.