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Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha)

Gomez-Uchida, Daniel, Seeb, Lisa W., Warheit, Kenneth I., McKinney, Garrett J., Seeb, James E.
Conservation genetics resources 2014 v.6 no.4 pp. 807-811
Oncorhynchus tshawytscha, biosynthesis, databases, fish, genes, high-throughput nucleotide sequencing, indigenous species, lipid metabolism, reproduction, single nucleotide polymorphism, stress response, transcriptome, transcriptomics
We deep-sequenced the transcriptome of Chinook salmon (Oncorhynchus tshawytscha) that yielded 2.5 million high-quality reads (combined for four fish) with an average length of 378 bp. De novo assembly resulted in 44,264 contigs with an average length of 567 bp and an average depth of 29 reads. Nearly half (42 %) of the contigs were annotated through alignment against protein, gene ontology (GO) and taxonomic databases using BLASTX. Overrepresented GO categories included metabolism (32 %), biosynthesis (11 %), transport (7 %), transcription (5 %) and other important pathways (response to stress, lipid metabolism and reproduction: 3 %). We identified 3,793 putative single nucleotide polymorphisms (SNPs) in silico, of which 718 were annotated. We characterized a sample of 54 annotated SNPs within contigs with transition-to-transversion ratios <1. Of these, 26 were nonsynonymous SNPs. Transcriptome sequencing remains a source of novel polymorphisms that holds promise for applied studies in Chinook salmon, an important salmonid species native to the North Pacific.