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Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.

Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X, Liu Z - BMC Genomics (2007)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA. jpquilang@gmail.com

ABSTRACT

Background: The 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).

Results: A 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

Conclusion: A 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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Related in: MedlinePlus

Gene Ontology (GO) assignment (3rd level GO terms) of 1,104 C. virginica annotated ESTs. The total numbers of ESTs annotated for each main category are 761 for Biological Process, 952 for Molecular Function, and 614 for Cellular Component. Since a gene product could be assigned to more than one GO term, the percentages in each main category do not add up to 100%.
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Figure 3: Gene Ontology (GO) assignment (3rd level GO terms) of 1,104 C. virginica annotated ESTs. The total numbers of ESTs annotated for each main category are 761 for Biological Process, 952 for Molecular Function, and 614 for Cellular Component. Since a gene product could be assigned to more than one GO term, the percentages in each main category do not add up to 100%.

Mentions: Gene Ontology (GO) categories were assigned to 1,104 unique ESTs with BLASTX hits using Blast2GO. Figure 3 shows the percentage distributions of gene ontology terms (3rd level GO terms) according to the GO consortium. Cellular physiological process (80 %) was the most dominant 3rd level term out of the 761 unique sequences which were annotated to the Biological Process GO category. This was followed by metabolism at 62%. Only 4% were assigned to the Biological Process subcategory response to stress. Protein binding (26%) was the most dominant out of 952 ESTs with significant protein hits which were assigned to Molecular Function category at 3rd level. This was followed by hydrolase activity and nucleotide binding at 17% each. GO terms at higher and lower levels for each of the three main GO categories as well as the unique ESTs which fall on each term are given in additional file 2.


Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.

Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X, Liu Z - BMC Genomics (2007)

Gene Ontology (GO) assignment (3rd level GO terms) of 1,104 C. virginica annotated ESTs. The total numbers of ESTs annotated for each main category are 761 for Biological Process, 952 for Molecular Function, and 614 for Cellular Component. Since a gene product could be assigned to more than one GO term, the percentages in each main category do not add up to 100%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919373&req=5

Figure 3: Gene Ontology (GO) assignment (3rd level GO terms) of 1,104 C. virginica annotated ESTs. The total numbers of ESTs annotated for each main category are 761 for Biological Process, 952 for Molecular Function, and 614 for Cellular Component. Since a gene product could be assigned to more than one GO term, the percentages in each main category do not add up to 100%.
Mentions: Gene Ontology (GO) categories were assigned to 1,104 unique ESTs with BLASTX hits using Blast2GO. Figure 3 shows the percentage distributions of gene ontology terms (3rd level GO terms) according to the GO consortium. Cellular physiological process (80 %) was the most dominant 3rd level term out of the 761 unique sequences which were annotated to the Biological Process GO category. This was followed by metabolism at 62%. Only 4% were assigned to the Biological Process subcategory response to stress. Protein binding (26%) was the most dominant out of 952 ESTs with significant protein hits which were assigned to Molecular Function category at 3rd level. This was followed by hydrolase activity and nucleotide binding at 17% each. GO terms at higher and lower levels for each of the three main GO categories as well as the unique ESTs which fall on each term are given in additional file 2.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA. jpquilang@gmail.com

ABSTRACT

Background: The 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).

Results: A 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

Conclusion: A 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.

Show MeSH
Related in: MedlinePlus