Figure 1: SWGA of Plasmodium parasites.

(a,b) Selection of SWGA primer sets. (a) The average distance (kb) between the 10,000 most frequent parasite motifs (colour coded by length) is plotted for both the P. falciparum (Pf3D7) and human (GRCh37) genomes. The red box highlights motifs that are spaced (on average) <50,000 bp apart in the P. falciparum, but >500,000 bp apart in the human genome. (b) Average distances between the sequence motifs shown in a, but plotted for the P. reichenowi (PrCDC) and chimpanzee (Pan_troglodytes-2.1.4) genomes. Red dots indicate all motifs that fall within the red box in a, with circles and stars denoting those selected for SWGA primer sets 6A and 8A, respectively (Supplementary Fig. 1). (c) Validation of the SWGA primer sets. Human genomic DNA spiked with known quantities of P. falciparum DNA (5–0.001%) was subjected to consecutive rounds of SWGA, using primer set 6A in the first and primer set 8A in the second round. The number of total base pairs (in millions) sequenced is shown in relation to the per cent coverage of the P. falciparum (Pf3D7) genome for five parasite concentrations. DNA mixtures were subjected to two independent amplifications, with individual and combined results shown in blue and red, respectively (the expected genome coverage without SWGA is shown in green). (d) MiSeq read depth for all 14 chromosomes across the Pf3D7 genome shown for one representative amplification at each of five parasite concentrations (individual chromosomes are drawn to scale as indicated on top). For each parasite/human DNA mixture, the percentage of P. falciparum and estimated number of genome copies are indicated. An expanded view of coverage across chromosome 9 is shown in Supplementary Fig. 2.