Abstract
BackgroundResearch using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations.ResultsIn this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster.ConclusionsThis study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.
Highlights
Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies
Of the 31,918 probes printed onto the array, 20,170 (63.2%) corresponded to annotated contigs in the GigasDatabase
Research on gene function and oyster physiology using real time PCR and microarray is becoming increasingly important and widespread. Because of their economic importance, evolutionary position and use as a model organism in environmental genomics, more research is being conducted on oyster species
Summary
Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. In July 2010, 56,268 EST sequences were compiled in the publicly accessible GigasDatabase version 6 housed at Sigenae (http://public-contigbrowser.sigenae.org:9090/ Crassostrea_gigas/index.html) [21] This genomic resource allows the development of genome wide microarrays for screening physiological traits and responses to the environment. These microarrays were used to describe gene expression patterns in response to heat stress [28] and hypoxia [29], and to compare oysters that were resistant or susceptible to summer mortalities [21] Since these studies were done, a large database of ESTs has become available, providing the information necessary to design a more comprehensive microarray suitable for characterizing genome-wide transcriptome profiles in Crassostrea gigas
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