Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it>
<p>Abstract</p> <p>Background</p> <p>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...
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| Format: | Article |
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BMC
2010-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/387 |
| _version_ | 1830447665440096256 |
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| author | Parrinello Hugues Dantec Christelle Beltran Sophie Cosseau Céline Grunau Christoph Portela Julien Boissier Jérôme |
| author_facet | Parrinello Hugues Dantec Christelle Beltran Sophie Cosseau Céline Grunau Christoph Portela Julien Boissier Jérôme |
| author_sort | Parrinello Hugues |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>Schistosoma mansoni</it>.</p> <p>Results</p> <p>Genomic DNA was extracted from male and female (heterogametic) <it>S. mansoni </it>adults and sequenced with a Genome Analyzer (Illumina). Sequences are available at the NCBI sequence read archive <url>http://www.ncbi.nlm.nih.gov/Traces/sra/</url> 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 <it>S. mansoni </it>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.</p> <p>Conclusion</p> <p>Our genome-to-genome comparison method that we call "whole-genome <it>in-silico </it>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 (<it>e.g</it>. strains, pathovars) or even closely related species.</p> |
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| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T07:25:35Z |
| publishDate | 2010-06-01 |
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| series | BMC Genomics |
| spelling | doaj.art-1dea0745c9d3453eb0153ad36c553fd12022-12-21T19:11:41ZengBMCBMC Genomics1471-21642010-06-0111138710.1186/1471-2164-11-387Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it>Parrinello HuguesDantec ChristelleBeltran SophieCosseau CélineGrunau ChristophPortela JulienBoissier Jérôme<p>Abstract</p> <p>Background</p> <p>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 <it>Schistosoma mansoni</it>.</p> <p>Results</p> <p>Genomic DNA was extracted from male and female (heterogametic) <it>S. mansoni </it>adults and sequenced with a Genome Analyzer (Illumina). Sequences are available at the NCBI sequence read archive <url>http://www.ncbi.nlm.nih.gov/Traces/sra/</url> 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 <it>S. mansoni </it>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.</p> <p>Conclusion</p> <p>Our genome-to-genome comparison method that we call "whole-genome <it>in-silico </it>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 (<it>e.g</it>. strains, pathovars) or even closely related species.</p>http://www.biomedcentral.com/1471-2164/11/387 |
| spellingShingle | Parrinello Hugues Dantec Christelle Beltran Sophie Cosseau Céline Grunau Christoph Portela Julien Boissier Jérôme Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> BMC Genomics |
| title | Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> |
| title_full | Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> |
| title_fullStr | Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> |
| title_full_unstemmed | Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> |
| title_short | Whole-genome <it>in-silico </it>subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of <it>Schistosoma mansoni</it> |
| title_sort | whole genome it in silico it subtractive hybridization wish using massive sequencing for the identification of unique and repetitive sex specific sequences the example of it schistosoma mansoni it |
| url | http://www.biomedcentral.com/1471-2164/11/387 |
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