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Background  The trematode flatworms of the genus  Schistosoma , the causative agents of schistosomiasis, are among the most prevalent parasites in humans, affecting more than 200 million people worldwide. In this study, we focused on two well-characterized strains of  S. mansoni , to explore signatures of selection. Both strains are highly inbred and exhibit differences in life history traits, in particular in their compatibility with the intermediate host  Biomphalaria glabrata .    Methodology/Principal Findings  We performed high throughput sequencing of DNA from pools of individuals of each strain using Illumina technology and identified single nucleotide polymorphisms (SNP) and copy number variations (CNV). In total, 708,898 SNPs were identified and roughly 2,000 CNVs. The SNPs revealed low nucleotide diversity (π = 2×10 −4 ) within each strain and a high differentiation level (Fst = 0.73) between them. Based on a recently developed  in-silico  approach, we further detected 12 and 19 private ( i.e.  specific non-overlapping) selective sweeps among the 121 and 151 sweeps found in total for each strain.    Conclusions/Significance  Functional annotation of transcripts lying in the private selective sweeps revealed specific selection for functions related to parasitic interaction ( e.g.  cell-cell adhesion or redox reactions). Despite high differentiation between strains, we identified evolutionary convergence of genes related to proteolysis, known as a key virulence factor and a potential target of drug and vaccine development. Our data show that pool-sequencing can be used for the detection of selective sweeps in parasite populations and enables one to identify biological functions under selection.

plos neglected tropical diseases

Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains