Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

Julien Portela,Jérôme Boissier,Christelle Dantec,Céline Cosseau,Sophie Beltran,Christoph Grunau,Hugues Parrinello

doi:10.1186/1471-2164-11-387

Abstract

BackgroundEmerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison). We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni.ResultsGenomic DNA was extracted from male and female (heterogametic) S. mansoni adults and sequenced with a Genome Analyzer (Illumina). Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome). The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome). Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite.ConclusionOur genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH) allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex). It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars) or even closely related species.

Highlights

Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains
We reasoned that male (ZZ) vs. female (ZW) whole genome comparison would enable to identify female specific sequences that are only present on the W chromosome
Mollusc infection consists in a simple contact in spring water between parasite larvae and molluscs, mouse infection is performed under general anaesthesia and parasite larvae penetrate naturally through the host skin

Summary

Introduction

Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. We propose a novel method to compare two genomes (genome-to-genome comparison). We used this method to identify sexspecific sequences of the human blood fluke Schistosoma mansoni. We reasoned that male (ZZ) vs female (ZW) whole genome comparison would enable to identify female specific sequences that are only present on the W chromosome. We split the bioinformatics analysis into two axes: one for the unique sequences and one for the repetitive sequences which allowed us to identify several new classes of female specific repeats and 105 contigs containing unique sequences

Results

Discussion

Conclusion