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

PLoS Neglected Tropical Diseases
Julie A J ClémentChristoph Grunau

Abstract

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. 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. 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 ...Continue Reading

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Citations

Sep 24, 2014·Nature Reviews. Genetics·Christian SchlöttererViola Nolte
Aug 11, 2015·Ecology and Evolution·Sarah P Flanagan, Adam G Jones
Oct 21, 2016·PLoS Neglected Tropical Diseases·James J CodyMichael H Hsieh
Jan 4, 2017·Trends in Parasitology·Céline CosseauChristoph Grunau
Feb 16, 2018·Genome Biology and Evolution·Julien Kincaid-SmithEve Toulza
Oct 16, 2015·PloS One·Marco FracassettiYvonne Willi
Jan 31, 2016·Molecular Ecology·David RoquisChristoph Grunau
Jul 6, 2016·Epigenetics & Chromatin·Sara FneichChristoph Grunau

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Datasets Mentioned

BETA
SRP016500
PRJNA177787

Methods Mentioned

BETA
pool-sequencing
Illumina sequencing
PCR
glycosylation
genotyping

Software Mentioned

GBrowse
cnv ’
Galaxy
Sequencher
fasta
Blast2GO
Interproscan
Seq Filter
gff
jar

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