ArticleBMC genomics2007
Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Development of SNP Panels as a New Tool to Assess the Genetic Diversity, Population Structure, and Parentage Analysis of the Eastern Oyster (Crassostrea virginica).Marine biotechnology (New York, N.Y.) · 2018Article
- Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).PloS one · 2017Article
- Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling.G3 (Bethesda, Md.) · 2016Article
- Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.PloS one · 2015Article
- Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica.BMC genomics · 2014Article
- Transcriptome analysis reveals a rich gene set related to innate immunity in the Eastern oyster (Crassostrea virginica).Marine biotechnology (New York, N.Y.) · 2014Article
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- Pyrosequencing of Haliotis diversicolor transcriptomes: insights into early developmental molluscan gene expression.PloS one · 2012Article
- De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing.PloS one · 2012Article
- Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum).BMC plant biology · 2011Article
- Development of expressed sequence tags from the pearl oyster, Pinctada martensii Dunker.Marine biotechnology (New York, N.Y.) · 2011Article
- Development of gene-targeted SNP markers for genomic mapping in Pacific abalone Haliotis discus hannai Ino.Molecular biology reports · 2010Article
- Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization.BMC genomics · 2010Article
- Identification of immune genes of the Agamaki clam (Sinonovacula constricta) by sequencing and bioinformatic analysis of ESTs.Marine biotechnology (New York, N.Y.) · 2010Article
- The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.).BMC plant biology · 2010Article
- Identification of CYP genes in Mytilus (mussel) and Crassostrea (oyster) species: first approach to the full complement of cytochrome P450 genes in bivalves.Marine environmental research · 2010Article
- Article
- Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1.BMC genomics · 2009Article
- A simple and efficient method for isolating polymorphic microsatellites from cDNA.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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