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Open Access Research article

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

Nolwenn M Dheilly12*, Christophe Lelong1, Arnaud Huvet2 and Pascal Favrel1

Author Affiliations

1 Université de Caen Basse-Normandie, UMR M100 "Physiologie et Ecophysiologie des Mollusques Marins", IBFA, IFR ICORE 146, Esplanade de la Paix, 14032 Caen Cedex, France

2 Ifremer, UMR M100 "Physiologie et Ecophysiologie des Mollusques Marins", Technopole Brest Iroise, 29290 Plouzané, France

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BMC Genomics 2011, 12:468  doi:10.1186/1471-2164-12-468

Published: 27 September 2011

Abstract

Background

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. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations.

Results

In 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.

Conclusions

This 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.