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
- Equal contributors
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
BMC Genomics 2010, 11:387 doi:10.1186/1471-2164-11-387Published: 21 June 2010
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.
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.
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.