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

Type Article
Date 2009-07
Language English
Author(s) Fleury ElodieORCID1, Huvet ArnaudORCID1, Lelong Christophe1, De Lorgeril Julien2, Boulo VivianeORCID2, Gueguen YannickORCID2, Bachere Evelyne2, Tanguy Arnaud3, Moraga Dario4, Fabioux Caroline4, Lindeque Penelope5, Shaw Jenny5, Reinhardt Richard6, Prunet Patrick7, Davey Grace8, Lapegue Sylvie9, Sauvage Christopher9, Corporeau Charlotte1, Moal Jeanne1, Gavory Frederick10, Wincker Patrick10, Moreews Francois11, Klopp Christophe11, Mathieu Michel1, Boudry PierreORCID, Favrel Pascal1
Affiliation(s) 1 : Univ Caen Basse Normandie, IFREMER, UMR Physiol & Ecophysiol Mollusques Marins M100, Ctr Brest, F-14032 Caen, France.
2 : Univ Montpellier 2, CNRS, IFREMER, UMR 5119,ECOLAG CC 80, F-34095 Montpellier 5, France.
3 : CNRS, UMR 7144, Stn Biol Roscoff, F-29682 Roscoff, France.
4 : Univ Bretagne Occidentale, Inst Univ Europeen Mer, CNRS, LEMAR,UMR 6539, F-29280 Plouzane, France.
5 : Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
6 : Max Planck Inst Mol Genet, D-14195 Berlin, Germany.
7 : INRA, SCRIBE, IFR 140, F-35000 Rennes, France.
8 : Natl Univ Ireland Galway, Natl Diagnost Ctr, Galway, Ireland.
9 : Ifremer, Lab Genet & Pathol, F-17390 La Tremblade, France.
10 : CEA, DSV, Ctr Natl Sequencage, F-91057 Evry, France.
11 : INRA, Sigenae Biometrie & Intelligence Artificielle UR8, F-31326 Castanet Tolosan, France.
Source BMC Genomics (1471-2164) (BioMed Central), 2009-07 , Vol. 10 , N. 341 , P. 1-15
DOI 10.1186/1471-2164-10-341
WOS© Times Cited 102
Abstract 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. Description: 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.htm l. 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. Conclusion: 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.
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Fleury Elodie, Huvet Arnaud, Lelong Christophe, De Lorgeril Julien, Boulo Viviane, Gueguen Yannick, Bachere Evelyne, Tanguy Arnaud, Moraga Dario, Fabioux Caroline, Lindeque Penelope, Shaw Jenny, Reinhardt Richard, Prunet Patrick, Davey Grace, Lapegue Sylvie, Sauvage Christopher, Corporeau Charlotte, Moal Jeanne, Gavory Frederick, Wincker Patrick, Moreews Francois, Klopp Christophe, Mathieu Michel, Boudry Pierre, Favrel Pascal (2009). 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. BMC Genomics, 10(341), 1-15. Publisher's official version : https://doi.org/10.1186/1471-2164-10-341 , Open Access version : https://archimer.ifremer.fr/doc/00000/6770/