Private selective sweeps identified from next-generation pool-sequencing reveal convergent pathways under selection in two inbred Schistosoma mansoni strains

Abstract

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.

Figure 1. Log 2 ratio plot of copy number variations (BRE/GH2) along the Schistosoma mansoni genome.

The x-axis represents the genome position in basepairs. Chromosomes are colour coded. The y-axis shows log2 ratio between BRE and GH2. Positive values indicate overrepresentation of a region in BRE, negative values indicate overrepresentation of a region in GH2.

Figure 2. Chromosomal representation of selective sweeps (in black) and non-swept regions (grey) over the 7 autosomes of Schistosoma mansoni for BRE and GH2.

Black arrowheads indicate the non-overlapping specific selective sweeps for both strains.