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Open Access Methodology article

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 Portela1, Christoph Grunau1, Céline Cosseau1, Sophie Beltran1, Christelle Dantec2, Hugues Parrinello2 and Jérôme Boissier1*

Author Affiliations

1 UMR 5244 CNRS-EPHE-UPVD. Parasitologie Fonctionnelle et Evolutive, CBETM. Université de Perpignan, Perpignan, France

2 Plateforme MGX, Institut de Génomique Fonctionnelle 141, rue de la Cardonille, Montpellier, France

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BMC Genomics 2010, 11:387  doi:10.1186/1471-2164-11-387

Published: 21 June 2010

Abstract

Background

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. 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.

Results

Genomic 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/ webcite 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.

Conclusion

Our 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.