GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas

Type Article
Date 2015-12
Language English
Author(s) Riviere Guillaume1, 2, Klopp Christophe3, Ibouniyamine Nabihoudine3, Huvet ArnaudORCID4, Boudry PierreORCID4, Favrel Pascal1, 2
Affiliation(s) 1 : Univ Caen, Inst Fundamental & Appl Biol, F-14032 Caen, France.
2 : Univ Caen, UMR BOREA Biol Organismes & Ecosyst Aquat, CNRS 7208, IRD 207,MNHN,UPMC,UCBN,UAG, F-14032 Caen, France.
3 : INRA, Sigenae Biometrie & Intelligence Artificielle UR8, F-31326 Castanet Tolosan, France.
4 : IFREMER, CNRS, UMR 6539, UBO,IRD,Lab Sci Environm Marin,ZI Pointe Diables, F-29280 Plouzane, France.
Source Bmc Bioinformatics (1471-2105) (Biomed Central Ltd), 2015-12 , Vol. 16 , N. 401 , P. 1-12
DOI 10.1186/s12859-015-0833-4
WOS© Times Cited 21
Keyword(s) Oyster, Transcriptome, Development, Stress, Tissues, NGS
Abstract 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.
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Riviere Guillaume, Klopp Christophe, Ibouniyamine Nabihoudine, Huvet Arnaud, Boudry Pierre, Favrel Pascal (2015). GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. Bmc Bioinformatics, 16(401), 1-12. Publisher's official version : https://doi.org/10.1186/s12859-015-0833-4 , Open Access version : https://archimer.ifremer.fr/doc/00302/41321/