Illuminating SNP Discovery and Population Genomics of Puget Sound Chinook Salmon Through the Transcriptome

We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchus tshawytscha) collected from four populations throughout Puget Sound (George Adams, Soos Creek, North Fork Stillaguamish, and Marblemount). Our goal was to use the transcriptome as a source of novel and informative single nucleotide polymorphisms (SNPs) that can discriminate between Puget Sound populations, known for their high value among recreational fishers and for their poor resolution using other genetic markers. Pyrosequencing yielded nearly 2.5 million of high-quality reads (combined for all four fish) with an average length of 378 bp, which were assembled de novo using 98% sequence similarity and 50% read overlap. De novo assembly generated 44,253 contiguous sequences (contigs) with an average length of 567 bp and an average depth of 29 reads. Contigs were annotated by running BLASTX against protein databases and by associating proteins to gene ontology (GO) terms using a relational database. GO analyses indicated that the Chinook salmon transcriptome was enriched for various categories, such as transcription, transport, development, and cell organization, within the Biological Process domain. We identified 10,698 putative SNPs, which await validation using a dedicated pipeline. Transcriptome sequencing remains a great source of novel polymorphisms that holds promise to resolve the shallow evolutionary history among Puget Sound Chinook salmon populations.