MPI für molekulare Genetik / Sequencing Group |
|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.|
|Authors:||Fleury, Elodie; Huvet, Arnaud; Lelong, Christophe; Lorgeril, Julien; Boulo, Viviane; Gueguen, Yannick; Bachère, Evelyne; Tanguy, Arnaud; Moraga, Dario; Fabioux, Caroline; Lindeque, Penelopee; Shaw, Jenny; Reinhardt, Richard; Prunet, Patrick; Davey, Grace; Lapègue, Sylvie; Sauvage, Christopher; Corporeau, Charlotte; Moal, Jeanne; Gavory, Frederick; Wincker, Patrick; Moreews, François; Klopp, Christophe; Mathieu, Michel; Boudry, Pierre; Favrel, Pascal|
|Research Context:||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-009) and "Gametogenes" (ANR-08-GENM-041).|
|Date of Publication (YYYY-MM-DD):||2009-07-29|
|Title of Journal:||BMC Genomics|
|Journal Abbrev.:||BMC Genomics|
|Copyright:||2009 Fleury et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
|Review Status:||not specified|
|Abstract / Description:||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.
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 webcite. 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.
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 hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.
|Comment of the Author/Creator:||corresponding author.
All sequence analyses were conducted in collaboration with the SIGENAE bioinformatics team. Specific requests for EST sequence chromatograms should be addressed at firstname.lastname@example.org.
|External Publication Status:||published|
|Communicated by:||Richard Reinhardt|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||1.UMR M100 Ifremer – Université de Caen Basse-Normandie « Physiologie et Ecophysiologie des Mollusques Marins », Centre de Brest, B.P. 70, 29280 Plouzané/IBFA, IFR ICORE 146, Esplanade de la Paix, 14032 Caen Cedex, France;
2.IFREMER CNRS Université de Montpellier 2, UMR 5119 ECOLAG CC 80, Place Eugène Bataillon, 34095 Montpellier cedex 5, France;
3.CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29682 Roscoff, France;
4.Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR-CNRS 6539, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Place Nicolas Copernic, 29280, Plouzané, France;
5.Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon PL1 3DH, UK;
6.Institut National de la Recherche Agronomique, INRA-SCRIBE, IFR 140, Campus de Beaulieu, 35000 Rennes, France;
7.National Diagnostics Centre, National University of Ireland Galway, Galway, Ireland;
8.Laboratoire de Génétique et Pathologie, Ifremer La Tremblade, 17390 La Tremblade, France;
9.CEA, DSV, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France;
1o.INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, BP 52627, 31326 Castanet-Tolosan Cedex, France.
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