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

Type Article
Date 2011-09
Language English
Author(s) Dheilly Nolwenn1, 2, Lelong Christophe1, Huvet ArnaudORCID2, Favrel Pascal1
Affiliation(s) 1 : Univ Caen Basse Normandie, UMR Physiol & Ecophysiol Mollusques Marins M100, IBFA, IFR ICORE 146, F-14032 Caen, France.
2 : IFREMER, UMR Physiol & Ecophysiol Mollusques Marins M100, F-29290 Plouzane, France.
Source Bmc Genomics (1471-2164) (Biomed Central Ltd), 2011-09 , Vol. 12 , P. -
DOI 10.1186/1471-2164-12-468
WOS© Times Cited 48
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 9arf1) 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.
Full Text
File Pages Size Access
Publisher's official version 17 3 MB Open access
Top of the page