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...
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ftdoajarticles:oai:doaj.org/article:9834a737f0d845829154796c443884b7 2023-05-15T15:58:22+02:00 Development of a Pacific oyster ( Crassostrea gigas ) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns Huvet Arnaud Lelong Christophe Dheilly Nolwenn M Favrel Pascal 2011-09-01T00:00:00Z https://doi.org/10.1186/1471-2164-12-468 https://doaj.org/article/9834a737f0d845829154796c443884b7 EN eng BMC http://www.biomedcentral.com/1471-2164/12/468 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-468 1471-2164 https://doaj.org/article/9834a737f0d845829154796c443884b7 BMC Genomics, Vol 12, Iss 1, p 468 (2011) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2011 ftdoajarticles https://doi.org/10.1186/1471-2164-12-468 2022-12-31T02:50:52Z 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 Directory of Open Access Journals: DOAJ Articles Pacific BMC Genomics 12 1 468 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 Huvet Arnaud Lelong Christophe Dheilly Nolwenn M Favrel Pascal Development of a Pacific oyster ( Crassostrea gigas ) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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 |
Huvet Arnaud Lelong Christophe Dheilly Nolwenn M Favrel Pascal |
author_facet |
Huvet Arnaud Lelong Christophe Dheilly Nolwenn M Favrel Pascal |
author_sort |
Huvet Arnaud |
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 |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1471-2164-12-468 https://doaj.org/article/9834a737f0d845829154796c443884b7 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
BMC Genomics, Vol 12, Iss 1, p 468 (2011) |
op_relation |
http://www.biomedcentral.com/1471-2164/12/468 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-468 1471-2164 https://doaj.org/article/9834a737f0d845829154796c443884b7 |
op_doi |
https://doi.org/10.1186/1471-2164-12-468 |
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BMC Genomics |
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12 |
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1 |
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468 |
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1766394092309184512 |