Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
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...
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ftarchimer:oai:archimer.ifremer.fr:15956 2023-05-15T15:58:15+02:00 Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns Dheilly, Nolwenn Lelong, Christophe Huvet, Arnaud Favrel, Pascal 2011-09 application/pdf https://archimer.ifremer.fr/doc/00048/15956/13397.pdf https://doi.org/10.1186/1471-2164-12-468 https://archimer.ifremer.fr/doc/00048/15956/ eng eng Biomed Central Ltd https://archimer.ifremer.fr/doc/00048/15956/13397.pdf doi:10.1186/1471-2164-12-468 https://archimer.ifremer.fr/doc/00048/15956/ 2011 Dheilly et al; licensee BioMed Central Ltd. info:eu-repo/semantics/openAccess restricted use Bmc Genomics (1471-2164) (Biomed Central Ltd), 2011-09 , Vol. 12 , P. - text Publication info:eu-repo/semantics/article 2011 ftarchimer https://doi.org/10.1186/1471-2164-12-468 2021-09-23T20:20:00Z 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Pacific BMC Genomics 12 1 468 |
institution |
Open Polar |
collection |
Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Dheilly, Nolwenn Lelong, Christophe Huvet, Arnaud Favrel, Pascal |
spellingShingle |
Dheilly, Nolwenn 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 Lelong, Christophe Huvet, Arnaud Favrel, Pascal |
author_sort |
Dheilly, Nolwenn |
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 |
https://archimer.ifremer.fr/doc/00048/15956/13397.pdf https://doi.org/10.1186/1471-2164-12-468 https://archimer.ifremer.fr/doc/00048/15956/ |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Bmc Genomics (1471-2164) (Biomed Central Ltd), 2011-09 , Vol. 12 , P. - |
op_relation |
https://archimer.ifremer.fr/doc/00048/15956/13397.pdf doi:10.1186/1471-2164-12-468 https://archimer.ifremer.fr/doc/00048/15956/ |
op_rights |
2011 Dheilly et al; licensee BioMed Central Ltd. info:eu-repo/semantics/openAccess restricted use |
op_doi |
https://doi.org/10.1186/1471-2164-12-468 |
container_title |
BMC Genomics |
container_volume |
12 |
container_issue |
1 |
container_start_page |
468 |
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1766393981960192000 |