Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns
<p>Abstract</p> <p>Background</p> <p>Research using the Pacific oyster <it>Crassostrea gigas </it>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 sequenc...
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| Format: | Article |
| Language: | English |
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BMC
2011-09-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/468 |
| _version_ | 1818551604935131136 |
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| 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 |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Research using the Pacific oyster <it>Crassostrea gigas </it>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.</p> <p>Results</p> <p>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. <it>Adp-ribosylation factor 1 </it>(<it>arf1</it>) 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.</p> <p>Conclusions</p> <p>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.</p> |
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| format | Article |
| id | doaj.art-9834a737f0d845829154796c443884b7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T09:02:07Z |
| publishDate | 2011-09-01 |
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| series | BMC Genomics |
| spelling | doaj.art-9834a737f0d845829154796c443884b72022-12-22T00:29:49ZengBMCBMC Genomics1471-21642011-09-0112146810.1186/1471-2164-12-468Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patternsHuvet ArnaudLelong ChristopheDheilly Nolwenn MFavrel Pascal<p>Abstract</p> <p>Background</p> <p>Research using the Pacific oyster <it>Crassostrea gigas </it>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.</p> <p>Results</p> <p>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. <it>Adp-ribosylation factor 1 </it>(<it>arf1</it>) 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/12/468 |
| spellingShingle | Huvet Arnaud Lelong Christophe Dheilly Nolwenn M Favrel Pascal Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns BMC Genomics |
| title | Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
| title_full | Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
| title_fullStr | Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
| title_full_unstemmed | Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
| title_short | Development of a Pacific oyster (<it>Crassostrea gigas</it>) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns |
| title_sort | development of a pacific oyster it crassostrea gigas it 31 918 feature microarray identification of reference genes and tissue enriched expression patterns |
| url | http://www.biomedcentral.com/1471-2164/12/468 |
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