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 C...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2009
|
Subjects: | |
Online Access: | http://hdl.handle.net/11858/00-001M-0000-0010-7D4B-F http://hdl.handle.net/11858/00-001M-0000-0010-7D4A-2 |
id |
ftpubman:oai:pure.mpg.de:item_1584118 |
---|---|
record_format |
openpolar |
spelling |
ftpubman:oai:pure.mpg.de:item_1584118 2024-09-15T18:03:07+00:00 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. BMC Genomics Fleury, E. Huvet, A. Lelong, C. Lorgeril, J. Boulo, V. Gueguen, Y. Bachère, E. Tanguy, A. Moraga, D. Fabioux, C. Lindeque, P. Shaw, J. Reinhardt, R. Prunet, P. Davey, G. Lapègue, S. Sauvage, C. Corporeau, C. Moal, J. Gavory, F. Wincker, P. Moreews, F. Klopp, C. Mathieu, M. Boudry, P. Favrel, P. 2009-07-29 application/pdf http://hdl.handle.net/11858/00-001M-0000-0010-7D4B-F http://hdl.handle.net/11858/00-001M-0000-0010-7D4A-2 eng eng info:eu-repo/semantics/altIdentifier/urn/http://www.biomedcentral.com/1471-2164/10/341 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-10-341 http://hdl.handle.net/11858/00-001M-0000-0010-7D4B-F http://hdl.handle.net/11858/00-001M-0000-0010-7D4A-2 info:eu-repo/semantics/openAccess BMC Genomics info:eu-repo/semantics/article 2009 ftpubman https://doi.org/10.1186/1471-2164-10-341 2024-07-31T09:31:27Z 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 webcite. 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 ... Article in Journal/Newspaper Crassostrea gigas Pacific oyster Max Planck Society: MPG.PuRe BMC Genomics 10 1 341 |
institution |
Open Polar |
collection |
Max Planck Society: MPG.PuRe |
op_collection_id |
ftpubman |
language |
English |
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 webcite. 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 ... |
format |
Article in Journal/Newspaper |
author |
Fleury, E. Huvet, A. Lelong, C. Lorgeril, J. Boulo, V. Gueguen, Y. Bachère, E. Tanguy, A. Moraga, D. Fabioux, C. Lindeque, P. Shaw, J. Reinhardt, R. Prunet, P. Davey, G. Lapègue, S. Sauvage, C. Corporeau, C. Moal, J. Gavory, F. Wincker, P. Moreews, F. Klopp, C. Mathieu, M. Boudry, P. Favrel, P. |
spellingShingle |
Fleury, E. Huvet, A. Lelong, C. Lorgeril, J. Boulo, V. Gueguen, Y. Bachère, E. Tanguy, A. Moraga, D. Fabioux, C. Lindeque, P. Shaw, J. Reinhardt, R. Prunet, P. Davey, G. Lapègue, S. Sauvage, C. Corporeau, C. Moal, J. Gavory, F. Wincker, P. Moreews, F. Klopp, C. Mathieu, M. Boudry, P. Favrel, P. 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. |
author_facet |
Fleury, E. Huvet, A. Lelong, C. Lorgeril, J. Boulo, V. Gueguen, Y. Bachère, E. Tanguy, A. Moraga, D. Fabioux, C. Lindeque, P. Shaw, J. Reinhardt, R. Prunet, P. Davey, G. Lapègue, S. Sauvage, C. Corporeau, C. Moal, J. Gavory, F. Wincker, P. Moreews, F. Klopp, C. Mathieu, M. Boudry, P. Favrel, P. |
author_sort |
Fleury, E. |
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://hdl.handle.net/11858/00-001M-0000-0010-7D4B-F http://hdl.handle.net/11858/00-001M-0000-0010-7D4A-2 |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
BMC Genomics |
op_relation |
info:eu-repo/semantics/altIdentifier/urn/http://www.biomedcentral.com/1471-2164/10/341 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-10-341 http://hdl.handle.net/11858/00-001M-0000-0010-7D4B-F http://hdl.handle.net/11858/00-001M-0000-0010-7D4A-2 |
op_rights |
info:eu-repo/semantics/openAccess |
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_ |
1810440634321862656 |