FN Archimer Export Format
PT J
TI 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
BT 
AF 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
AS 1:1;2:1;3:1;4:2;5:2;6:2;7:2;8:3;9:4;10:4;11:5;12:5;13:6;14:7;15:8;16:9;17:9;18:1;19:1;20:10;21:10;22:11;23:11;24:1;25:;26:1;
FF 1:PDG-DOP-DCB-PFOM-PI;2:PDG-DOP-DCB-PFOM-PI;3:;4:PDG-DOP-DCM-BOME-LALR;5:PDG-DOP-DCM-BOME-LALR;6:PDG-DOP-DCOP-AQUAPOL-LBQP;7:PDG-DOP-DCM-BOME;8:;9:;10:;11:;12:;13:;14:;15:;16:PDG-DOP-DCN-AGSAE-LGP;17:PDG-DOP-DCN-AGSAE-LGP;18:PDG-DOP-DCB-PFOM-PI;19:PDG-DOP-DCB-PFOM-PI;20:;21:;22:;23:;24:;25:PDG-DOP-DCB-PFOM-PI;26:;
C1 Univ Caen Basse Normandie, IFREMER, UMR Physiol & Ecophysiol Mollusques Marins M100, Ctr Brest, F-14032 Caen, France.
   Univ Montpellier 2, CNRS, IFREMER, UMR 5119,ECOLAG CC 80, F-34095 Montpellier 5, France.
   CNRS, UMR 7144, Stn Biol Roscoff, F-29682 Roscoff, France.
   Univ Bretagne Occidentale, Inst Univ Europeen Mer, CNRS, LEMAR,UMR 6539, F-29280 Plouzane, France.
   Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   Max Planck Inst Mol Genet, D-14195 Berlin, Germany.
   INRA, SCRIBE, IFR 140, F-35000 Rennes, France.
   Natl Univ Ireland Galway, Natl Diagnost Ctr, Galway, Ireland.
   Ifremer, Lab Genet & Pathol, F-17390 La Tremblade, France.
   CEA, DSV, Ctr Natl Sequencage, F-91057 Evry, France.
   INRA, Sigenae Biometrie & Intelligence Artificielle UR8, F-31326 Castanet Tolosan, France.
C2 UNIV CAEN, FRANCE
   UNIV MONTPELLIER, FRANCE
   CNRS, FRANCE
   UBO, FRANCE
   PML, UK
   INST MAX PLANCK (MOL GENET), GERMANY
   INRA, FRANCE
   UNIV NATL IRELAND, IRELAND
   IFREMER, FRANCE
   CEA, FRANCE
   INRA, FRANCE
SI BREST
   MONTPELLIER
   TAHITI
   PALAVAS
   LA TREMBLADE
SE PDG-DOP-DCB-PFOM-PI
   PDG-DOP-DCM-BOME-LALR
   PDG-DOP-DCOP-AQUAPOL-LBQP
   PDG-DOP-DCM-BOME
   PDG-DOP-DCN-AGSAE-LGP
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-p187
   copubli-europe
   copubli-univ-france
IF 3.759
TC 115
UR https://archimer.ifremer.fr/doc/2009/publication-6770.pdf
LA English
DT Article
AB 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.
PY 2009
PD JUN
SO BMC Genomics
SN 1471-2164
PU BioMed Central
VL 10
IS 341
UT 000269509300001
BP 1
EP 15
DI 10.1186/1471-2164-10-341
ID 6770
ER

EF