title: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Julie A J
authors.initials: JA
authors.lastname: Clément
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Eve
authors.initials: E
authors.lastname: Toulza
authors.affiliation: INRA, UMR CBGP (INRA - IRD - Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gautier
authors.affiliation: MGX Montpellier GenomiX, Montpellier, France.
authors.forename: Hugues
authors.initials: H
authors.lastname: Parrinello
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: David
authors.initials: D
authors.lastname: Roquis
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Boissier
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Rognon
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Moné
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Mouahid
authors.affiliation: CNRS, Institut de Génétique Humaine, UPR 1142, Montpellier, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Buard
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Mitta
authors.affiliation: Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France ; CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France.
authors.forename: Christoph
authors.initials: C
authors.lastname: Grunau
mesh_terms: D000818:Animals; D001700:Biomphalaria; D019295:Computational Biology; D006224:Cricetinae; D019143:Evolution, Molecular; D018628:Gene Dosage; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D012550:Schistosoma mansoni / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA