Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

Abstract

BackgroundAlthough bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available.DescriptionIn the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster.ConclusionA publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Functional characterization of a short neuropeptide F-related receptor in a Lophotrochozoa, the mollusk Crassostrea gigas

“…Unfortunately, no sNPF-like peptides with a characteristic Cterminal RLRFamide motif were found. A similar RPRFamide pattern was detected in oyster mature NPY/F, originating from a full-length NPY/F precursor (CU983945) that was identified in GigasDatabase (Fleury et al, 2009), and in some of its truncated forms characterized by mass spectrometry (MS) (data not shown). These peptides were tested in addition to a set of FMRFamide-like neuropeptides, carrying the RFamide motif that is generally thought to be essential for receptor activation in this peptide family (Kulathila et al, 1999).…”

“…Because of the availability of extended transcriptome resources (Fleury et al, 2009) and the recent availability of its genome sequence (Zhang et al, 2012), the Pacific oyster Crassostrea gigas (Thunberg 1793) has become an interesting model to investigate the evolution of regulatory pathways in Lophotrochozoa, one of the three major clades of bilaterian animals. In the present study, we identified a GPCR from C. gigas that is phylogenetically closely related to sNPFRs, and found its specific activation by a distinct family of RFamide-related peptides with potential involvement in the control of feeding, energy metabolism and reproduction.…”

Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacleBalanus amphitrite

“…It was possible to annotate around 20% (966/4843) of isotigs of the adult with a GO number, with this proportion reduced to 11% (743/6754) and 8% (623/7506) for the cypris and naupliar stages, respectively. These are relatively low percentages, reflecting the paucity of genetic information for the whole Vericrustacea (ex Maxillopoda) class, but yet not far from previous investigations (Fleury et al 2009;Bettencourt et al 2010). As expected, most of the GO hits within the 'Biological Processes' category from each assembly matched translation-related transcripts (eg ribosomal proteins).…”

The evolution and comparative neurobiology of endocannabinoid signalling

“…Furthermore, transcriptomic/genomic sequence data are available for molluscan species, including the gastropod A. californica [132] and the bivalve Crassostrea gigas [133]. Therefore, identification of genes encoding proteins implicated in endocannabinoid signalling (e.g.…”