Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for
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TECHNICAL NOTE
Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha) Daniel Gomez-Uchida • Lisa W. Seeb • Kenneth I. Warheit • Garrett J. McKinney James E. Seeb
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Received: 16 May 2014 / Accepted: 19 May 2014 Ó Springer Science+Business Media Dordrecht 2014
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. Keywords Chinook salmon Transcriptome sequencing Transcriptome assembly Single nucleotide polymorphisms
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0235-3) contains supplementary material, which is available to authorized users. D. Gomez-Uchida (&) L. W. Seeb K. I. Warheit G. J. McKinney J. E. Seeb School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195-5020, USA e-mail: [email protected] L. W. Seeb e-mail: [email protected] G. J. McKinney e-mail: [email protected] J. E. Seeb e-mail: [email protected] Present Address: D. Gomez-Uchida Department of Zoology & Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepcio´n, Casilla 160-C, Concepcio´n, Chile K. I. Warheit Washington Department of Fish and Wildlife, 600 Capitol Way N., Olympia, WA 98501-1091, USA e-mail: [email protected]
Transcriptome sequencing provides databases that yield insights into expressed genes that mediate important biological processes (Willette et al. 2014). In addition to applications related to differential gene expression (Gavery and Roberts 2012), variation at the transcriptional level has accelerated the discovery of markers for use in population genetics studies, such as single nucleotide polymorphisms (SNPs) (Roberts et al. 2012; Seeb et al. 2011). Chinook salmon (Oncorhynchus tshawytscha) is one of the most iconic salmonids in the Pacific Northwest, USA, where it supports a vast fishing community. Many Chinook salmon populations face considerable conservation challen
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