Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ

Giulia Micallef, Ralph Bickerdike, Caroline Reiff, Jorge M O Fernandes, Alan S Bowman, Samuel A M Martin

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)559-569
Number of pages11
JournalMarine Biotechnology
Volume14
Issue number5
Early online date19 Apr 2012
DOIs
Publication statusPublished - Oct 2012

Fingerprint

Salmo salar
mucins
Transcriptome
skin (animal)
transcriptome
Mucins
skin
Salmon
salmon
Skin
Messenger RNA
gene
genes
Genes
Biological Phenomena
expressed sequence tags
transcriptomics
mucus
bioinformatics
Data Mining

Keywords

  • 454-sequencing
  • mucin
  • aquaculture
  • skin

Cite this

Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. / Micallef, Giulia; Bickerdike, Ralph; Reiff, Caroline; Fernandes, Jorge M O; Bowman, Alan S; Martin, Samuel A M.

In: Marine Biotechnology, Vol. 14, No. 5, 10.2012, p. 559-569.

Research output: Contribution to journalArticle

Micallef, Giulia ; Bickerdike, Ralph ; Reiff, Caroline ; Fernandes, Jorge M O ; Bowman, Alan S ; Martin, Samuel A M. / Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. In: Marine Biotechnology. 2012 ; Vol. 14, No. 5. pp. 559-569.
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