A Systematic Map of Genetic Variation in Plasmodium falciparum

Abstract

Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in the development of new effective vaccines and in the appropriate use of antimalarial drugs. By performing a full-genome scan of allelic variability in 14 field and laboratory strains of P. falciparum, we comprehensively identified ≈500 genes evolving at higher than neutral rates. The majority of the most variable genes have paralogs within the P. falciparum genome and may be subject to a different evolutionary clock than those without. The group of 211 variable genes without paralogs contains most known immunogens and a few drug targets, consistent with the idea that the human immune system and drug use is driving parasite evolution. We also reveal gene-amplification events including one surrounding pfmdr1, the P. falciparum multidrug-resistance gene, and a previously uncharacterized amplification centered around the P. falciparum GTP cyclohydrolase gene, the first enzyme in the folate biosynthesis pathway. Although GTP cyclohydrolase is not the known target of any current drugs, downstream members of the pathway are targeted by several widely used antimalarials. We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs.

Diversity and evolution of the rhoph1/clag multigene family of Plasmodium falciparum

“…The high polymorphism observed in clag2, 3.1, and 3.2 is consistent with the observation by Kidgell et al [40] based on the hybridization of genomic DNA from a panel of parasite lines to an oligonucleotide array for the P. falciparum genome. In addition, the polymorphism levels are comparable to those of the microneme proteins such as eba-175 (π = 0.0030; d N = 0.0037) and ama-1 (π = 0.0166; d N = 0.0207), which are exposed to host immune responses [17,18].…”

Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes

“…There are more SNPs (12 nonsynonymous and 0 synonymous) in the chloroquine resistance transporter (pfcrt) in assorted P. falciparum isolates relative to what would be expected by chance without considering the resistance or sensitivity phenotype (36,37). Indeed, after excluding nonconserved, membrane-localized or antigenic proteins, pfcrt remains one of the most variable in the P. falciparum genome (33,36,37). Thus, well-characterized genes conserved across species with higher rates of nonsynonymous SNPs will often have roles in drug resistance.…”

“…In P. falciparum, genes that produce the most abundant proteins in sporozoites have been investigated as vaccine candidates (49,50). In addition, these pre-erythrocytic vaccine candidates show evidence of higher-thanexpected variability in P. falciparum (33). We thus sought to classify the most highly variable and highly expressed transcripts for the P. vivax sporozoite stage (Table S4).…”

“…Genetic diversity studies have been useful in P. falciparum for rapidly identifying genomic regions in linkage disequilibrium following selection for drug-resistant parasites (33,36). In addition, microarray-based genetic diversity studies of P. falciparum identified the amplification of GTP cyclohydrolase I (pfgch1, PFL1155w) and suggested it as a marker for antifolate resistance (33). These types of studies are particularly needed in P. vivax as there is evidence of the emergence of resistance to chloroquine, which is widely used as a first-line treatment, and the mechanisms of chloroquine action and resistance are fundamentally Fig.…”

“…Once identified, the global geographic distribution of drug resistance genes can help inform treatment policy. In addition, genetic diversity studies can provide information on the variability of possible vaccine candidates as has been shown in P. falciparum (33,36,37,52).…”