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Background  The Mediterranean mussel ( Mytilus galloprovincialis ) is a cosmopolitan, cultured bivalve with worldwide commercial and ecological importance. However, there is a qualitative and quantitative lack of knowledge of the molecular mechanisms involved in the physiology and immune response of this mollusc. In order to start filling this gap, we have studied the transcriptome of mantle, muscle and gills from naïve Mediterranean mussels and hemocytes exposed to distinct stimuli.    Results  A total of 393,316 million raw RNA-Seq reads were obtained and assembled into 151,320 non-redundant transcripts with an average length of 570 bp. Only 55 % of the transcripts were shared across all tissues. Hemocyte and gill transcriptomes shared 60 % of the transcripts while mantle and muscle transcriptomes were most similar, with 77 % shared transcripts. Stimulated hemocytes showed abundant defense and immune-related proteins, in particular, an extremely high amount of antimicrobial peptides. Gills expressed many transcripts assigned to both structure and recognition of non-self patterns, while in mantle many transcripts were related to reproduction and shell formation. Moreover, this tissue presented additional and interesting hematopoietic, antifungal and sensorial functions. Finally, muscle expressed many myofibril and calcium-related proteins and was found to be unexpectedly associated with defense functions. In addition, many metabolic routes related to cancer were represented.    Conclusions  Our analyses indicate that whereas the transcriptomes of these four tissues have characteristic expression profiles in agreement with their biological structures and expected functions, tissue-specific transcriptomes reveal a complex and specialized functions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1817-5) contains supplementary material, which is available to authorized users.

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues