title: GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.
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.
  
  
  METHODS
  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.
authors.affiliation: Institute for fundamental and applied biology, University of Caen Basse-Normandie, Caen, France. guillaume.riviere@unicaen.fr.|UMR BOREA 'Biologie des organismes et écosystèmes aquatiques', Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, Caen, F-14032, France. guillaume.riviere@unicaen.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Riviere
authors.affiliation: INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, BP 52627, Castanet-Tolosan Cedex, 31326, France. christophe.klopp@toulouse.inra.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, BP 52627, Castanet-Tolosan Cedex, 31326, France. nabihoudine.ibounyamine@toulouse.inra.fr.
authors.forename: Nabihoudine
authors.initials: N
authors.lastname: Ibouniyamine
authors.affiliation: Ifremer, UMR CNRS 6539 (CNRS/UBO/IRD/Ifremer), Laboratoire des Sciences de l'Environnement Marin, ZI de la Pointe du Diable, CS 10070, Plouzané, 29280, France. arnaud.huvet@ifremer.fr.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Huvet
authors.affiliation: Ifremer, UMR CNRS 6539 (CNRS/UBO/IRD/Ifremer), Laboratoire des Sciences de l'Environnement Marin, ZI de la Pointe du Diable, CS 10070, Plouzané, 29280, France. pierre.boudry@ifremer.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Boudry
authors.affiliation: Institute for fundamental and applied biology, University of Caen Basse-Normandie, Caen, France. pascal.favrel@unicaen.fr.|UMR BOREA 'Biologie des organismes et écosystèmes aquatiques', Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, Caen, F-14032, France. pascal.favrel@unicaen.fr.
authors.forename: Pascal
authors.initials: P
authors.lastname: Favrel
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D049896:Crassostrea / Q000235:genetics*; D030541:Databases, Genetic; D015723:Gene Library; D063990:Gene Ontology; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome