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Exome sequencing in Atlantic salmon
Ane Gro Siri SkjelfjordThe main goal of this proposal is to exploit the forthcoming reference genome sequence, together with the wealth of transcriptome data, to develop a whole genome exon capture array for Atlantic salmon (Salmo salar).
Prosjektleder: Sigbjørn Lien
This work will activate a predictably very successful collaboration between Centre for Integrative Genetics (CIGENE) at the Norwegian University of Life Sciences and Craig Venter Institute (JCVI), located in Rockville, MD, recently awarded Phase II in the salmon genome sequencing.
Development of an exon capture array for Atlantic salmon will be an important tool for large-scale characterization of exonic sequences and gene copy number variation (CNV) in both Atlantic salmon and the closely related brown trout. Obvious applications of the array are improved accuracy in variant detection and evidence-based gene prediction, as well as better separation and characterization of duplicated regions in the regions in the Atlantic salmon genome. Development of a whole genome exon capture array is a major bioinformatics challenge connecting researchers from JCVI and CIGENE. Funding of the application will allow researcher in the two groups to visit each other for shorter periods. It will give us access to a unique computational infrastructure and key bioinformatics competence at JCVI.
Subgoals of the project:
Use the exon capture array, together with NGS technology, to carry out large-scale variant discovery in populations of Atlantic salmon
Develop a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of exome sequencing data in Atlantic salmon
Test the exome capture array in populations of the closely related brown trout
Oppdatert: 09.05.12
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