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Conservation Genetics Resources

, Volume 6, Issue 4, pp 807–811 | Cite as

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-UchidaEmail author
  • Lisa W. Seeb
  • Kenneth I. Warheit
  • Garrett J. McKinney
  • James E. Seeb
Technical Note

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 

Notes

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.

Supplementary material

12686_2014_235_MOESM1_ESM.pdf (174 kb)
Supplementary material 1 (PDF 174 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Daniel Gomez-Uchida
    • 1
    • 2
    Email author
  • Lisa W. Seeb
    • 1
  • Kenneth I. Warheit
    • 1
    • 3
  • Garrett J. McKinney
    • 1
  • James E. Seeb
    • 1
  1. 1.School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleUSA
  2. 2.Department of Zoology & Interdisciplinary Center for Aquaculture Research (INCAR)Universidad de ConcepciónConcepciónChile
  3. 3.Washington Department of Fish and WildlifeOlympiaUSA

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