GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
International audience Background: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism amon...
Published in: | BMC Bioinformatics |
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Main Authors: | , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2015
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Subjects: | |
Online Access: | https://hal.sorbonne-universite.fr/hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440/document https://hal.sorbonne-universite.fr/hal-01258440/file/BMC1.pdf https://doi.org/10.1186/s12859-015-0833-4 |
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Institut national des sciences de l'Univers: HAL-INSU |
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English |
topic |
NGS Development Tissues ACL Stress Oyster Transcriptome [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
NGS Development Tissues ACL Stress Oyster Transcriptome [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere [SDE.BE]Environmental Sciences/Biodiversity and Ecology Riviere, Guillaume Klopp, Christophe, C. Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
topic_facet |
NGS Development Tissues ACL Stress Oyster Transcriptome [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
International audience Background: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. Description: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. Conclusions: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists. |
author2 |
Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA) Institut de Biologie Fondamentale et Appliquée Caen (IBFA) Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) Institut National de la Recherche Agronomique (INRA) 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) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Agence Nationale de la Recherche ANR-08-GENM-04 'Gametogenes' ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) |
format |
Article in Journal/Newspaper |
author |
Riviere, Guillaume Klopp, Christophe, C. Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal |
author_facet |
Riviere, Guillaume Klopp, Christophe, C. Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal |
author_sort |
Riviere, Guillaume |
title |
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
title_short |
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
title_full |
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
title_fullStr |
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
title_full_unstemmed |
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas |
title_sort |
gigaton: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster crassostrea gigas |
publisher |
HAL CCSD |
publishDate |
2015 |
url |
https://hal.sorbonne-universite.fr/hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440/document https://hal.sorbonne-universite.fr/hal-01258440/file/BMC1.pdf https://doi.org/10.1186/s12859-015-0833-4 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
ISSN: 1471-2105 BMC Bioinformatics https://hal.sorbonne-universite.fr/hal-01258440 BMC Bioinformatics, 2015, 16, pp.401. ⟨10.1186/s12859-015-0833-4⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-015-0833-4 info:eu-repo/semantics/altIdentifier/pmid/26627443 hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440/document https://hal.sorbonne-universite.fr/hal-01258440/file/BMC1.pdf doi:10.1186/s12859-015-0833-4 PRODINRA: 346626 PUBMED: 26627443 WOS: 000365651000001 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s12859-015-0833-4 |
container_title |
BMC Bioinformatics |
container_volume |
16 |
container_issue |
1 |
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1796308204193316864 |
spelling |
ftinsu:oai:HAL:hal-01258440v1 2024-04-14T08:10:35+00:00 GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas Riviere, Guillaume Klopp, Christophe, C. Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA) Institut de Biologie Fondamentale et Appliquée Caen (IBFA) Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) Institut National de la Recherche Agronomique (INRA) 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) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Agence Nationale de la Recherche ANR-08-GENM-04 'Gametogenes' ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) 2015-12-02 https://hal.sorbonne-universite.fr/hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440/document https://hal.sorbonne-universite.fr/hal-01258440/file/BMC1.pdf https://doi.org/10.1186/s12859-015-0833-4 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-015-0833-4 info:eu-repo/semantics/altIdentifier/pmid/26627443 hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440 https://hal.sorbonne-universite.fr/hal-01258440/document https://hal.sorbonne-universite.fr/hal-01258440/file/BMC1.pdf doi:10.1186/s12859-015-0833-4 PRODINRA: 346626 PUBMED: 26627443 WOS: 000365651000001 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1471-2105 BMC Bioinformatics https://hal.sorbonne-universite.fr/hal-01258440 BMC Bioinformatics, 2015, 16, pp.401. ⟨10.1186/s12859-015-0833-4⟩ NGS Development Tissues ACL Stress Oyster Transcriptome [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2015 ftinsu https://doi.org/10.1186/s12859-015-0833-4 2024-03-21T17:24:28Z International audience Background: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. Description: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. Conclusions: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Institut national des sciences de l'Univers: HAL-INSU Pacific BMC Bioinformatics 16 1 |