Library Prep and Sequencing

We used whole-genome amplification of single miracidia dried on FTA cards followed by exome capture and sequencing (Illumina 2500) to generate genome-wide sequence data following methods described in Le Clec’h et al. (2018). The exome capture probe set (SureSelect design ID: S0742423) was designed using the published reference genome sequence for S. haematobium (SchHae_1.0, GCA_000699445.1, lab strain, originally from Egypt). The exome capture probe set included 156,004,120-bp RNA baits from the nuclear genome and 67 from the mitochondrial genome, covering 96% (62,106/64,642) of the exons and accounting for 94% of the exome length (15,002,706 bp/15,895,612 bp). Each captured exon was covered by an average of 2.59 120-bp baits (Le Clec’h et al. 2018).

In addition to exome capture, we generated whole-genome sequence data for twelve samples, six from each population (Niger and Zanzibar). Libraries were multiplexed and paired end 150-bp reads were sequenced on a single Illumina NextSeq flowcell. In addition to the whole-genome and exome sequence data generated above, we gathered available genome sequence data from the NCBI Short Read Archives for six other species of Schistosoma in the haematobium group, including S. bovis (ERR119622, ERR103048, and ERR539853), S. curassoni (ERR310937 and ERR119623), S. haematobium (ERR084970, ERR037800, and SRR433865), S. intercalatum (ERR539854, ERR539856, and ERR119613), S. guineensis (ERR119612, ERR539850, and ERR539852), S. mattheei (ERR539851, ERR539855, ERR539857, and ERR103051), and S. margrebowiei (ERR310940) in 20 separate libraries (Young et al. 2012; Coghlan et al. 2019).