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
International audience 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...
Published in: | BMC Genomics |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2009
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Online Access: | https://inria.hal.science/inria-00435769 https://inria.hal.science/inria-00435769/document https://inria.hal.science/inria-00435769/file/art_10.1186_1471-2164-10-341.pdf https://doi.org/10.1186/1471-2164-10-341 |
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ftnormandieuniv:oai:HAL:inria-00435769v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Normandie Université: HAL |
op_collection_id |
ftnormandieuniv |
language |
English |
topic |
structure du génome génomique base de données [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN]Life Sciences [q-bio]/Genetics |
spellingShingle |
structure du génome génomique base de données [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN]Life Sciences [q-bio]/Genetics 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 Lapegue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédérick, F. Wincker, Patrick Moreews, François Klopp, Christophe, C. 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 [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN]Life Sciences [q-bio]/Genetics |
description |
International audience 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 ... |
author2 |
Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL) Unité Littoral (LITTORAL) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Physiologie et Ecophysiologie des Mollusques Marins (PE2M) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG) Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Adaptation et diversité en milieu marin (ADMM) Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR) Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Université de Brest (UBO) Plymouth Marine Laboratory (PML) Max-Planck-Institut für Molekulare Genetik (MPIMG) Max-Planck-Gesellschaft Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE) Institut National de la Recherche Agronomique (INRA) Génétique fonctionnelle, agronomie et santé IFR 140 (GFAS) Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) National Diagnostics Centre (NDC) National University of Ireland Galway (NUI Galway) Unité Amélioration génétique, Santé animale et Environnement (AGSAE) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Biological systems and models, bioinformatics and sequences (SYMBIOSE) Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA) Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique Institut National de Recherche en Informatique et en Automatique (Inria) Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH) Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes Système d'Information des GENomes des Animaux d'Elevage (SIGENAE) Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) Laboratoire de Physiologie des Invertébrés (LPI) Physiologie Fonctionnelle des Organismes Marins (PFOM) The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project "Aquafirst" (513692) in the Sixth Framework Program, ANR "CgPhysiogène" (ANR-06-GANI-0009) and "Gametogenes" (ANR-08-GENM-041) ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006) ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) |
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 Lapegue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédérick, F. Wincker, Patrick Moreews, François Klopp, Christophe, C. 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 Lapegue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédérick, F. Wincker, Patrick Moreews, François Klopp, Christophe, C. 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 |
HAL CCSD |
publishDate |
2009 |
url |
https://inria.hal.science/inria-00435769 https://inria.hal.science/inria-00435769/document https://inria.hal.science/inria-00435769/file/art_10.1186_1471-2164-10-341.pdf https://doi.org/10.1186/1471-2164-10-341 |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
ISSN: 1471-2164 BMC Genomics https://inria.hal.science/inria-00435769 BMC Genomics, 2009, 10 (341), pp.341. ⟨10.1186/1471-2164-10-341⟩ http://www.biomedcentral.com/bmcgenomics |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-10-341 inria-00435769 https://inria.hal.science/inria-00435769 https://inria.hal.science/inria-00435769/document https://inria.hal.science/inria-00435769/file/art_10.1186_1471-2164-10-341.pdf doi:10.1186/1471-2164-10-341 PRODINRA: 32341 WOS: 000269509300001 |
op_rights |
http://creativecommons.org/licenses/by/ 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 |
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1796941053882793984 |
spelling |
ftnormandieuniv:oai:HAL:inria-00435769v1 2024-04-21T08:00:35+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 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 Lapegue, Sylvie Sauvage, Christopher Corporeau, Charlotte Moal, Jeanne Gavory, Frédérick, F. Wincker, Patrick Moreews, François Klopp, Christophe, C. Mathieu, Michel Boudry, Pierre Favrel, Pascal Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL) Unité Littoral (LITTORAL) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Physiologie et Ecophysiologie des Mollusques Marins (PE2M) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG) Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Adaptation et diversité en milieu marin (ADMM) Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR) Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Université de Brest (UBO) Plymouth Marine Laboratory (PML) Max-Planck-Institut für Molekulare Genetik (MPIMG) Max-Planck-Gesellschaft Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE) Institut National de la Recherche Agronomique (INRA) Génétique fonctionnelle, agronomie et santé IFR 140 (GFAS) Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) National Diagnostics Centre (NDC) National University of Ireland Galway (NUI Galway) Unité Amélioration génétique, Santé animale et Environnement (AGSAE) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Biological systems and models, bioinformatics and sequences (SYMBIOSE) Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA) Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique Institut National de Recherche en Informatique et en Automatique (Inria) Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH) Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes Système d'Information des GENomes des Animaux d'Elevage (SIGENAE) Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) Laboratoire de Physiologie des Invertébrés (LPI) Physiologie Fonctionnelle des Organismes Marins (PFOM) The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project "Aquafirst" (513692) in the Sixth Framework Program, ANR "CgPhysiogène" (ANR-06-GANI-0009) and "Gametogenes" (ANR-08-GENM-041) ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006) ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) 2009-07-29 https://inria.hal.science/inria-00435769 https://inria.hal.science/inria-00435769/document https://inria.hal.science/inria-00435769/file/art_10.1186_1471-2164-10-341.pdf https://doi.org/10.1186/1471-2164-10-341 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-10-341 inria-00435769 https://inria.hal.science/inria-00435769 https://inria.hal.science/inria-00435769/document https://inria.hal.science/inria-00435769/file/art_10.1186_1471-2164-10-341.pdf doi:10.1186/1471-2164-10-341 PRODINRA: 32341 WOS: 000269509300001 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1471-2164 BMC Genomics https://inria.hal.science/inria-00435769 BMC Genomics, 2009, 10 (341), pp.341. ⟨10.1186/1471-2164-10-341⟩ http://www.biomedcentral.com/bmcgenomics structure du génome génomique base de données [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN]Life Sciences [q-bio]/Genetics info:eu-repo/semantics/article Journal articles 2009 ftnormandieuniv https://doi.org/10.1186/1471-2164-10-341 2024-04-11T00:41:14Z International audience 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 ... Article in Journal/Newspaper Crassostrea gigas Pacific oyster Normandie Université: HAL BMC Genomics 10 1 341 |