Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
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...
Main Authors: | , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BioMed Central Ltd.
2011
|
Subjects: | |
Online Access: | http://www.biomedcentral.com/1471-2164/12/468 |
id |
ftbiomed:oai:biomedcentral.com:1471-2164-12-468 |
---|---|
record_format |
openpolar |
spelling |
ftbiomed:oai:biomedcentral.com:1471-2164-12-468 2023-05-15T15:58:17+02:00 Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns Dheilly, Nolwenn M Lelong, Christophe Huvet, Arnaud Favrel, Pascal 2011-09-27 http://www.biomedcentral.com/1471-2164/12/468 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2164/12/468 Copyright 2011 Dheilly et al; licensee BioMed Central Ltd. Research article 2011 ftbiomed 2011-10-15T23:43:42Z 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster BioMed Central Pacific |
institution |
Open Polar |
collection |
BioMed Central |
op_collection_id |
ftbiomed |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Dheilly, Nolwenn M Lelong, Christophe Huvet, Arnaud Favrel, Pascal |
spellingShingle |
Dheilly, Nolwenn M Lelong, Christophe Huvet, Arnaud Favrel, Pascal Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
author_facet |
Dheilly, Nolwenn M Lelong, Christophe Huvet, Arnaud Favrel, Pascal |
author_sort |
Dheilly, Nolwenn M |
title |
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
title_short |
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
title_full |
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
title_fullStr |
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
title_full_unstemmed |
Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
title_sort |
development of a pacific oyster (crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
publisher |
BioMed Central Ltd. |
publishDate |
2011 |
url |
http://www.biomedcentral.com/1471-2164/12/468 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
http://www.biomedcentral.com/1471-2164/12/468 |
op_rights |
Copyright 2011 Dheilly et al; licensee BioMed Central Ltd. |
_version_ |
1766394008699928576 |