Genotyping recombinant Plasmodium parasites

Cloned parasites were initially typed with 10 microsatellites to screen for potential recombinant progeny as described^{36 (link)} using primers in Supplementary Table 2. DNA labeling and hybridization to a custom-made SNP-typing microarray were conducted essentially as described using 1 μg of gDNA^{27 (link)}. Scanned images were gridded and processed using NimbleGen v2.5 (Roche NimbleGen Inc.) to extract signal data. SNP genotypes were called when the probe sets at each locus indicated complementary SNP genotypes on both DNA strands. Parental clones were also hybridized in duplicate, and genotypes were scored at each locus as inheriting one of the parental genotypes or as N/A if a non-parental genotype was called. A total of 60 progeny with unique microsatellite patterns were genotyped with the SNP array.