GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
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...
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fttriple:oai:gotriple.eu:10670/1.bbdw7x 2023-05-15T15:57:37+02:00 GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas Riviere, Guillaume Klopp, Christophe Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal https://doi.org/10.1186/s12859-015-0833-4 https://archimer.ifremer.fr/doc/00302/41321/40520.pdf https://archimer.ifremer.fr/doc/00302/41321/ en eng Biomed Central Ltd doi:10.1186/s12859-015-0833-4 10670/1.bbdw7x https://archimer.ifremer.fr/doc/00302/41321/40520.pdf https://archimer.ifremer.fr/doc/00302/41321/ other Archimer, archive institutionnelle de l'Ifremer Bmc Bioinformatics (1471-2105) (Biomed Central Ltd), 2015-12 , Vol. 16 , N. 401 , P. 1-12 envir info Text https://vocabularies.coar-repositories.org/resource_types/c_18cf/ fttriple https://doi.org/10.1186/s12859-015-0833-4 2023-01-22T18:37:00Z 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. Text Crassostrea gigas Pacific oyster Unknown Pacific BMC Bioinformatics 16 1 |
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envir info Riviere, Guillaume Klopp, Christophe 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 |
envir info |
description |
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. |
format |
Text |
author |
Riviere, Guillaume Klopp, Christophe Ibouniyamine, Nabihoudine Huvet, Arnaud Boudry, Pierre Favrel, Pascal |
author_facet |
Riviere, Guillaume Klopp, Christophe 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 |
Biomed Central Ltd |
url |
https://doi.org/10.1186/s12859-015-0833-4 https://archimer.ifremer.fr/doc/00302/41321/40520.pdf https://archimer.ifremer.fr/doc/00302/41321/ |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Archimer, archive institutionnelle de l'Ifremer Bmc Bioinformatics (1471-2105) (Biomed Central Ltd), 2015-12 , Vol. 16 , N. 401 , P. 1-12 |
op_relation |
doi:10.1186/s12859-015-0833-4 10670/1.bbdw7x https://archimer.ifremer.fr/doc/00302/41321/40520.pdf https://archimer.ifremer.fr/doc/00302/41321/ |
op_rights |
other |
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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1766393298033836032 |