Abstract
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.
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Acknowledgments
Eleni Petrou and Sewall Young helped in the field. We thank Washington Department of Fish and Wildlife hatcheries facilities for samples. Carita Pascal and Jesse Tsai assisted during laboratory stages. Meredith Everett provided the Perl script to parse BLASTX hits. Funding from N08-12 High-resolution SNPs for identification of poorly differentiated stocks (Pacific Salmon Commission's Chinook Technical Committee (US section) for Funding under the letter of Agreement, LOA), Washington State General Fund (to KIW), Gordon and Betty Moore Foundation (to LWS and JES), and FONDAP 15110027 from Chile’s CONICYT (to DG-U) are greatly appreciated.
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Gomez-Uchida, D., Seeb, L.W., Warheit, K.I. et al. Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha). Conservation Genet Resour 6, 807–811 (2014). https://doi.org/10.1007/s12686-014-0235-3
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DOI: https://doi.org/10.1007/s12686-014-0235-3