Identifying SNPs in Rainbow Trout Paralogs

With up to four whole genome duplications, the trout genome is one of the most complex in the animal kingdom. For this reason SNP discovery in Rainbow Trout remains a difficult task due to the abundance of paralogous genes and repetitive sequence. One strategy of SNP discovery is to throw out paralogous sequence by aligning sequence to a genome, but without a sequenced genome, trout researchers are unable to utilize such a strategy. With the abundance of trout paralogs this strategy would likely limit the number of genes where SNPs could be detected anyway. For these reasons a different approach was developed to identify SNPs in paralogs from cDNA produced using next generation sequencing. Validation was performed on a subset of the predicted SNPs using genomic DNA. This approach may be useful to researchers studying expression of paralogs or to researchers studying organisms with whole genome duplications.