Abstract
BackgroundThe Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam.ResultsA normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring.ConclusionsThe transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.
Highlights
The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems
A signal ratio < 3 and a minimum of fluorescence >100 was recorded for 223 (1.6%) probe-pairs in the gills and 151 (1%) probe-pairs in the digestive gland. These results suggested that natural antisense transcripts (NATs) may be present in the clam transcriptome
Whole-transcriptome analysis holds the promise to shed light on the genetic mechanisms underlying cellular and organismal response to physiological and pathological conditions. This is of particular importance for improved shellfish aquaculture and for cost-effective environmental monitoring
Summary
The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. Harvest of R. philippinarum has experienced a dramatic increase in the last 20 years, currently representing one of the major aquacultured species in the world (3.36 million metric tons in 2008). Despite the relevance of Manila clam landings in world aquaculture, genomic resources for R. philippinarum are still extremely limited [2]. A genomic analysis was recently used to investigate summer mortality in the Pacific oyster [4]. To this end, the development of transcriptomic tools for the Manila clam is the first necessary step
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