Genomics in bivalve aquaculture

Molecular studies of non-model organisms have always been complicated by a substantial lack of genetic and genomic knowledge. Knowledge on the expressed genes can solve questions of great interest in the aquaculture field, including the identification of molecular markers of disease and transcriptional signatures of various stress factors. The progresses of sequencing technologies has led to the sequencing of oyster genome and transcriptomes of other bivalves. This information could potentially provide useful hints for improving many aspects of broodstock management and disease monitoring. As a key example, here we present the most recent goals achieved in the genomic study of the Mediterranean mussel Mytilus galloprovincialis through the long-lasting collaboration between the Universities of Trieste and Padova. The de novo assembly of M. galloprovincialis can rely on the existence of about 300 million Illumina sequencing reads, in addition to several rounds of 454 Life Sciences RNA-seq and the pre-existing data included in Mytibase. The assembly of about 110K contigs was a good basis to improve the understanding of mussel genes, their organization and functional role. We report in more detail the experience done in specific cases of study: The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: A widespread and diverse family of immune-related molecules (Dev Comp Immunol 35:635-643, 2011). Big defensins and mytimacins, new AMP families of the Mediterranean mussel Mytilus galloprovincialis (Dev Comp Immunol 36:390-399, 2012). Toll-like receptors and MyD88 adaptors in Mytilus: Complete cds and gene expression levels. (Dev Comp Immunol 40:158-166, 2013). RNA-seq and de novo digestive gland transcriptome assembly of the mussel Mytilus galloprovincialis provide insights on mussel response to paralytic shellfish poisoning (submitted 2014)