Development of Exome Capture Sequencing for the Atlantic Salmon (Salmo salar)

Background: Atlantic salmon (salmo salar) is an important species contributing to local and global economies through aquaculture, wild stock fisheries and recreational sport fisheries. As a cost-reducing alternative to whole-genome sequencing, we wanted to establish exome capture sequencing to identify protein-coding variants in Atlantic salmon. Development of an exome capture array for Atlantic salmon will be useful for large-scale characterization of exonic sequences and gene copy number variation (CNV) in both Atlantic salmon and the closely related brown trout. Such studies will be instrumental for obtaining a better understanding of the global patterns of inter-genomic and intra-species coding sequence divergence and its impact on gene function.

Results: We designed a probe set to capture exonic regions using an in-house developed annotation, CIGENE annotation version 2, targeting 89.7 Mb of the genome. Roche produced a NimbleGen SeqCap EZ chip, and we sequenced 475 Atlantic salmon and four rainbow trout. After filtering, we identify on average 240k SNPs and 23k indels for each sample.

Conclusion: Exome capture sequencing can be a cost-effective way of identifying protein-coding variations in Atlantic salmon.