Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase
Background: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster...
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Online Access: | http://prodinra.inra.fr/ft/00F55106-69FA-4B1D-96B6-123990B85CD2 http://prodinra.inra.fr/record/32341 https://doi.org/10.1186/1471-2164-10-341 |
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ftinraparis:oai:prodinra.inra.fr:32341 2023-05-15T15:57:49+02:00 Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase Fleury, Elodie Huvet, Arnaud Lelong, Christophe de Lorgeril, Julien Boulo, Viviane Gueguen, Yannick Bachère, Evelyne Tanguy, Arnaud Moraga, Dario Fabioux, Caroline Lindeque, Penelope Shaw, Jenny Reinhardt, Richard Prunet, Patrick Davey, Grace Lapègue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédéric Wincker, Patrick Moreews, François Klopp, Christophe Mathieu, Michel Boudry, Pierre Favrel, Pascal 2009 application/pdf http://prodinra.inra.fr/ft/00F55106-69FA-4B1D-96B6-123990B85CD2 http://prodinra.inra.fr/record/32341 https://doi.org/10.1186/1471-2164-10-341 eng eng http://creativecommons.org/licenses/by-nd-nc/1.0/ CC-BY-ND-NC BMC Genomics 341 (10), 1-15. (2009) structure du génome;génomique;base de données crustacea coquillage crassostrea gigas huître génome génomique fonctionnelle base de données expression des gènes ARTICLE 2009 ftinraparis https://doi.org/10.1186/1471-2164-10-341 2015-11-10T23:26:50Z Background: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description: In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion: A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Institut National de la Recherche Agronomique: ProdINRA Pacific BMC Genomics 10 1 341 |
institution |
Open Polar |
collection |
Institut National de la Recherche Agronomique: ProdINRA |
op_collection_id |
ftinraparis |
language |
English |
topic |
structure du génome;génomique;base de données crustacea coquillage crassostrea gigas huître génome génomique fonctionnelle base de données expression des gènes |
spellingShingle |
structure du génome;génomique;base de données crustacea coquillage crassostrea gigas huître génome génomique fonctionnelle base de données expression des gènes Fleury, Elodie Huvet, Arnaud Lelong, Christophe de Lorgeril, Julien Boulo, Viviane Gueguen, Yannick Bachère, Evelyne Tanguy, Arnaud Moraga, Dario Fabioux, Caroline Lindeque, Penelope Shaw, Jenny Reinhardt, Richard Prunet, Patrick Davey, Grace Lapègue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédéric Wincker, Patrick Moreews, François Klopp, Christophe Mathieu, Michel Boudry, Pierre Favrel, Pascal Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
topic_facet |
structure du génome;génomique;base de données crustacea coquillage crassostrea gigas huître génome génomique fonctionnelle base de données expression des gènes |
description |
Background: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description: In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion: A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism. |
format |
Article in Journal/Newspaper |
author |
Fleury, Elodie Huvet, Arnaud Lelong, Christophe de Lorgeril, Julien Boulo, Viviane Gueguen, Yannick Bachère, Evelyne Tanguy, Arnaud Moraga, Dario Fabioux, Caroline Lindeque, Penelope Shaw, Jenny Reinhardt, Richard Prunet, Patrick Davey, Grace Lapègue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédéric Wincker, Patrick Moreews, François Klopp, Christophe Mathieu, Michel Boudry, Pierre Favrel, Pascal |
author_facet |
Fleury, Elodie Huvet, Arnaud Lelong, Christophe de Lorgeril, Julien Boulo, Viviane Gueguen, Yannick Bachère, Evelyne Tanguy, Arnaud Moraga, Dario Fabioux, Caroline Lindeque, Penelope Shaw, Jenny Reinhardt, Richard Prunet, Patrick Davey, Grace Lapègue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédéric Wincker, Patrick Moreews, François Klopp, Christophe Mathieu, Michel Boudry, Pierre Favrel, Pascal |
author_sort |
Fleury, Elodie |
title |
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
title_short |
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
title_full |
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
title_fullStr |
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
title_full_unstemmed |
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase |
title_sort |
generation and analysis of a 29,745 unique expressed sequence tags from the pacific oyster (crassostrea gigas) assembled into a publicly accessible database: the gigasdatabase |
publishDate |
2009 |
url |
http://prodinra.inra.fr/ft/00F55106-69FA-4B1D-96B6-123990B85CD2 http://prodinra.inra.fr/record/32341 https://doi.org/10.1186/1471-2164-10-341 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
BMC Genomics 341 (10), 1-15. (2009) |
op_rights |
http://creativecommons.org/licenses/by-nd-nc/1.0/ |
op_rightsnorm |
CC-BY-ND-NC |
op_doi |
https://doi.org/10.1186/1471-2164-10-341 |
container_title |
BMC Genomics |
container_volume |
10 |
container_issue |
1 |
container_start_page |
341 |
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1766393511424294912 |