Abstract
BackgroundThe eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST) resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs).ResultsA normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174) of the unique ESTs had significant hits (E-value ≤ 1e-05) to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO) terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters.ConclusionA high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the material basis for future microarray development, marker validation, and genetic linkage and QTL analysis.
Highlights
The eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America
Using the sequenced expressed sequence tag (EST), along with those ESTs already existing in the GenBank, we identified 6,533 single nucleotide polymorphic sites that are potentially useful for genetic linkage mapping and QTL analysis in this species
A high-quality normalized/subtracted cDNA library was constructed as determined by the high gene discovery rate (84.6%) with over 6,000 clones of ESTs being sequenced
Summary
The eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. Lawrence in Canada to the Gulf of Mexico, Caribbean, and coasts of Brazil and Argentina [1] This species has been introduced to the Pacific coast of North America, Europe, and Hawaii but it has maintained reproducing populations in only two localities outside its natural range, namely, in a river in British Columbia and in a small basin in Hawaii [2]. It thrives in estuaries and coastal areas and is present in some areas as extensive reefs. Outbreak of major diseases such as Dermo (caused by a protozoan pathogen, Perkinsus marinus) and MSX (Multinucleate Sphere X, caused by another protozoan Haplosporidium nelsoni) have devastated both farmed and wild populations of the oyster species
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
