Development of Target Enrichment Strategies for Pacific Salmon and Trout Genomics

As sequencing technology advances, more next-generation sequencing tools and data have become available to the developing field of population genomics. Several new methods are now available for the preparation of targeted regions of genomes, allowing questions requiring larger sample sizes to be more affordably addressed. We present here a method for the development of probes for solution hybrid selection in the genus Oncorhynchus. Using transcriptome data from chum salmon, over 25k probes for putative exons were identified. Additional exons were targeted from similar data for rainbow trout, Sockeye salmon, and Chinook salmon. Two classes of probes are described from the data: probes which captured genomic DNA across all species, and probes which were species specific. A general salmonid target enrichment set for phylogenetic comparisons and a chum salmon target enrichment set  for population genomics were then developed. Flexible probe set design allowed the inclusion of SNP loci currently used for population genetics to test sequence data quality and for backwards compatibility with existing data sets. Capture efficiency, read depth, and the number of SNPs present in the different data sets are discussed.