Figure 5 | Scientific Reports

Figure 5

From: Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

Figure 5

Mutually exclusive large allelic deletions on chromosome 9 within the high FST window between gdv1 and gexp22. (A) Map of a 60 kb region of the chromosome (from position 1,370,000–1,430,000) marking the individual genes, and zoom into a 5 kb part of the intragenic region of the reference 3D7 sequence. The position of the highest FST SNP is shown with an asterisk. The PacBio long-read sequence pileup of the region from six P. falciparum isolates shows the two allelic deletion blocks, termed the 3D7 type (1.5 kb deletion outlined in red) and Dd2 type (1 kb deletion in blue). PacBio sequencing of the closely related species P. reichenowi identified the presence of both insert blocks, indicating the deletion event occurred subsequent to the separation of these two species. (B) Map showing pie charts of the frequencies of the alternative allelic deletion alleles across West Africa, 3D7 reference type (red) and Dd2 type (blue). Short read data from single genotype infections were mapped to a partial chromosome 9 reference containing both the 3D7 and Dd2 insert types, allowing proportions of alleles to be determined at all except one of the local populations (Faranah in Guinea for which mapped read depths were too low for most isolates). The deletion alleles were in strong overall linkage disequilibrium (LD) with the alleles at the highest FST SNP (D′ = 0.91, r2 = 0.61), a similar association seen within most of the local populations analysed separately (mean D′ = 0.93, mean r2 = 0.53).