Abstract
BackgroundThe Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis.ResultsA database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed.ConclusionsThis study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.
Highlights
The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view
European clam aquaculture production is centered in three major species of clams: Ruditapes philippinarum, the manila clam, Ruditapes decussatus, the grooved carpet shell clam and Venerupis pullastra, the pullet carpet shell clam
According to FAO and Fishstat reports, most of the relevant increases of production have been concentrated in R. philippinarum and R. decussatus, both of which have been severely affected by perkinsosis during the last years
Summary
The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. Historical records show that R. decussatus was one of the major aquaculture species in Europe, but due to overfishing, recruitment failures and some outbreaks of bacterial infection and parasitism, producers started to substitute this species for a closer but exotic clam from the same family, the manila clam R. philippinarum [1]. The introduction of this species, with a faster growing rate and believed to be more resistant to some diseases, originated a progressive replacement of the native clam and nowadays the production of grooved carpet shell clam is almost insignificant in most Mediterranean countries. Perkinsus is considered a model organism to understand adaptations to parasitism [2]
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