Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in IndianPlasmodium vivaxisolates

Abstract

SUMMARYWith a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite,Plasmodium vivax, we utilized the published whole genome sequence information ofP. falciparumandP. vivaxto find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) inP. vivaxin this syntenic region. PCR ofP. vivaxisolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies inP. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of IndianP. vivax.