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Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

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Abstract

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally >10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

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Acknowledgements

The research was supported by a studentship to G. Micallef funded by BioMar Ltd. The authors would like to thank Dr. William Roy and Dr. Andrew Tildesley for their assistance with fish handling at the MERL in Machrihanish.

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Authors and Affiliations

  1. Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK

    Giulia Micallef, Alan S. Bowman & Samuel A. M. Martin

  2. BioMar Ltd, Grangemouth Docks, Grangemouth, FK3 8UL, UK

    Ralph Bickerdike

  3. School of Medicine & Dentistry, Division of Applied Medicine, University of Aberdeen, Polwarth Building, Aberdeen, AB24 2ZD, UK

    Caroline Reiff

  4. Faculty of Biosciences and Aquaculture, University of Nordland, 8049, Bodø, Norway

    Jorge M. O. Fernandes

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  1. Giulia Micallef
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  2. Ralph Bickerdike
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  4. Jorge M. O. Fernandes
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  5. Alan S. Bowman
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  6. Samuel A. M. Martin
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Correspondence to Samuel A. M. Martin.

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A.S. Bowman and S.A.M. Martin contributed equally to the work.

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Micallef, G., Bickerdike, R., Reiff, C. et al. Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ. Mar Biotechnol 14, 559–569 (2012). https://doi.org/10.1007/s10126-012-9447-2

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  • DOI: https://doi.org/10.1007/s10126-012-9447-2

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