mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The 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. Results A 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. Conclusions This 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.

Gill net and longlines fisheries in Cyclades waters (Aegean Sea): species composition and gear competition

Species composition and gear competition for the small-scale fisheries in the Cyclades waters (off Naxos Island, Aegean Sea. Hellas) was studied based on samples collected during 1997-1998 with gill nets of different mesh sizes and longlines with hooks of different sizes. Comparisons used univariate and multivariate techniques based on species compositions by number and weight and the commercial/total catch ratio in terms of weight and number. The results of the various techniques were in agreement and suggested that the different gear/size/season combinations fall into two groups (all gill nets and all longlines), which differed from each other in terms of species composition. species diversity and dominance. In contrast, the commercial/total catch ratio did not differ either within and between gears. The implications of the results for the management of the Mediterranean fisheries resources are also discussed. (C) 2002 Elsevier Science B.V. All rights reserved.