Sequencing and Characterization of Striped Venus Transcriptome Expand Resources for Clam Fishery Genetics

Abstract

BackgroundThe striped venus Chamelea gallina clam fishery is among the oldest and the largest in the Mediterranean Sea, particularly in the inshore waters of northern Adriatic Sea. The high fishing pressure has lead to a strong stock abundance decline, enhanced by several irregular mortality events. The nearly complete lack of molecular characterization limits the available genetic resources for C. gallina. We achieved the first transcriptome of this species with the aim of identifying an informative set of expressed genes, potential markers to assess genetic structure of natural populations and molecular resources for pathogenic contamination detection.Methodology/Principal FindingsThe 454-pyrosequencing of a normalized cDNA library of a pool C. gallina adult individuals yielded 298,494 raw reads. Different steps of reads assembly and filtering produced 36,422 contigs of high quality, one half of which (18,196) were annotated by similarity. A total of 111 microsatellites and 20,377 putative SNPs were identified. A panel of 13 polymorphic transcript-linked microsatellites was developed and their variability assessed in 12 individuals. Remarkably, a scan to search for contamination sequences of infectious origin indicated the presence of several Vibrionales species reported to be among the most frequent clam pathogen's species. Results reported in this study were included in a dedicated database available at http://compgen.bio.unipd.it/chameleabase.Conclusions/SignificanceThis study represents the first attempt to sequence and de novo annotate the transcriptome of the clam C. gallina. The availability of this transcriptome opens new perspectives in the study of biochemical and physiological role of gene products and their responses to large and small-scale environmental stress in C. gallina, with high throughput experiments such as custom microarray or targeted re-sequencing. Molecular markers, such as the already optimized EST-linked microsatellites and the discovered SNPs will be useful to estimate effects of demographic processes and to detect minute levels of population structuring.

Bivalve transcriptomics reveal pathogen sequences and a powerful immune response of the Mediterranean mussel (Mytilus galloprovincialis)

“…Sequencing, assembly, and annotation results are summarized in Table 1 and Fig S1. Raw read statistics and quality measures are summarized in Fig S2. Briefly, the sequencing of the stimulated hemocytes from M. galloprovincialis, M. edulis, and R. decussatus resulted in a combined total of more than 400,000 reads, of which 86.5% for M. galloprovincialis, 85.2% for M. edulis, and 78% for R. decussatus passed the first filtering and quality control test. The number of reads obtained in these transcriptomes was in agreement with numbers previously obtained for other molluscs using one-half of a picotiter plate on the 454 GS FLX system (Coppe et al 2012;Milan et al 2011), and it was even greater than the number obtained from high-throughput sequencing approaches performed for other mollusc species (Galindo et al 2010;Shi et al 2013).…”

Development of Molecular Resources for an Intertidal Clam, Sinonovacula constricta, Using 454 Transcriptome Sequencing

“…The transcriptomes of three other Veneridae family bivalve species, C. gallina [43], M. meretrix [23], and R. philippinarum [44], previously sequenced on the 454 platform were downloaded from NCBI. These datasets included 165,283 C. gallina reads, 35,004 M. meretrix contigs and 457,667 R. philippinarum reads.…”

Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

“…Their membership in the phylum Mollusca is undisputed and bivalve monophyly, although challenged in early molecular analyses, has found support in more recent studies using large datasets. Bivalve species have become the focus of numerous lines of interdisciplinary research, including the recent publication of the draft genomes of two pteriomorphian species (Takeuchi et al 2012;Zhang et al 2012) and new transcriptomic resources (Clark et al 2010;Kocot et al 2011;Milan et al 2011;Smith et al 2011;Coppe et al 2012). Translational medical studies on bivalves include aging research (Ungvari et al 2011) and the discovery of new antibiotics produced by the bacterial gill symbionts of shipworms (Elshahawi et al 2013).…”