Similarities between the R. philippinarum transcriptome and another four bivalve species sequences were analyzed by comparative genomics (Crassostrea gigas of the family Ostreidae, Bathymodiolus azoricus and Mytilus galloprovincialis of the family Mytilidae and Laternula elliptica of the family Laternulidae). This analysis could identify specific transcripts that are conserved in these five species. A Venn diagram was constructed using unique sequences from these databases according to the gene identifier (gi id number) of each sequence in its respective database: 207,764 from C. gigas, 76,055 from B. azoricus, 121,318 from M. galloprovincialis and 1,034,379 from L. elliptica. C. gigas was chosen because is the most represented bivalve species in the public databases. The other three species are bivalves that have been studied in transcriptomic assays. Figure 5 shows that of the total 29,679 clusters, 72% were found exclusively in the R. philippinarum group, while only 7.59% shared significant similarity with all five species. The number of coincidences among other groups was very low (4.14% to 0.31% of sequences), suggesting that 21,454 new sequences were discovered within the bivalve group. The percentage of new sequences is very high compared to previous transcriptomic studies [33] [34] , in which the fraction of new transcripts was approximately 45%. One possible explanation for this discrepancy is the low number of nucleotide and EST sequences currently available in public databases for R. philippinarum, but these transcripts could also be regions in which homology is not reached, such as 59 and 39 untranslated regions or genes with a high mutation rate. On the other hand, a comparison between our 454 results and the Milan et al. [16] transcriptome using a BLASTn approach is summarized in Table 2 Immune-related sequences R. philippinarum hemocytes were subjected to immune stimulation using several different PAMPs to enrich the EST collection with immune-related sequences. The objective was to obtain a more complete view of clam responses to pathogens. A keyword list and GO immune-related terms were used to find proteins putatively involved in the immune system. After this selection step, we found that more than 10% of the proteins predicted from the contig sequences had a possible immune function. Some sequences were found to be clustered in common, well-recognized immune pathways, such as the complement, apoptosis and toll-like receptors pathways, indicating conserved ancient mechanisms in bivalves ( Figures 6, 7, 8 ).