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...
Published in: | BMC Genomics |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | unknown |
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Springer Nature
2009
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Subjects: | |
Online Access: | http://hdl.handle.net/10379/11519 https://doi.org/10.1186/1471-2164-10-341 |
id |
ftnuigalway:oai:aran.library.nuigalway.ie/:10379/11519 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
National University of Ireland (NUI), Galway: ARAN |
op_collection_id |
ftnuigalway |
language |
unknown |
topic |
single nucleotide polymorphisms factor-beta superfamily genome annotation summer mortality cell-development marine genomics energy-balance linkage maps kappa-b identification |
spellingShingle |
single nucleotide polymorphisms factor-beta superfamily genome annotation summer mortality cell-development marine genomics energy-balance linkage maps kappa-b identification 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, Frederick 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 |
single nucleotide polymorphisms factor-beta superfamily genome annotation summer mortality cell-development marine genomics energy-balance linkage maps kappa-b identification |
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 ... |
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, Frederick 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, Frederick 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 |
publisher |
Springer Nature |
publishDate |
2009 |
url |
http://hdl.handle.net/10379/11519 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_relation |
BMC Genomics 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, Frederick; Wincker, Patrick; Moreews, François; Klopp, Christophe; Mathieu, Michel; Boudry, Pierre; Favrel, Pascal (2009). 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. BMC Genomics 10 , 1471-2164 http://hdl.handle.net/10379/11519 doi:10.1186/1471-2164-10-341 |
op_rights |
Attribution-NonCommercial-NoDerivs 3.0 Ireland https://creativecommons.org/licenses/by-nc-nd/3.0/ie/ |
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 |
_version_ |
1768385919938723840 |
spelling |
ftnuigalway:oai:aran.library.nuigalway.ie/:10379/11519 2023-06-11T04:11:04+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, Frederick Wincker, Patrick Moreews, François Klopp, Christophe Mathieu, Michel Boudry, Pierre Favrel, Pascal 2009-01-01 http://hdl.handle.net/10379/11519 https://doi.org/10.1186/1471-2164-10-341 unknown Springer Nature BMC Genomics 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, Frederick; Wincker, Patrick; Moreews, François; Klopp, Christophe; Mathieu, Michel; Boudry, Pierre; Favrel, Pascal (2009). 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. BMC Genomics 10 , 1471-2164 http://hdl.handle.net/10379/11519 doi:10.1186/1471-2164-10-341 Attribution-NonCommercial-NoDerivs 3.0 Ireland https://creativecommons.org/licenses/by-nc-nd/3.0/ie/ single nucleotide polymorphisms factor-beta superfamily genome annotation summer mortality cell-development marine genomics energy-balance linkage maps kappa-b identification Article 2009 ftnuigalway https://doi.org/10.1186/1471-2164-10-341 2023-05-28T18:05:18Z 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 ... Article in Journal/Newspaper Crassostrea gigas Pacific oyster National University of Ireland (NUI), Galway: ARAN Pacific BMC Genomics 10 1 341 |