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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 72.
Published online Feb 9, 2009. doi:  10.1186/1471-2164-10-72
PMCID: PMC2657158
MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences
Paola Venier,#1 Cristiano De Pittà,#1,2 Filippo Bernante,1,2 Laura Varotto,1 Barbara De Nardi,3 Giuseppe Bovo,4 Philippe Roch,5 Beatriz Novoa,6 Antonio Figueras,6 Alberto Pallavicini,corresponding author7 and Gerolamo Lanfranchicorresponding author1,2
1Department of Biology, University of Padova, Via U Bassi, 58/B, 35121, Padova, Italy
2C.R.I.B.I. Biotechnology Centre, University of Padova, Via U Bassi, 58/B, 35121, Padova, Italy
3Council for Research and Experimentation in Agriculture, Viale XXVIII Aprile, 26, 31015 Conegliano, Treviso, Italy
4Institue of Veterinary Sciences (IZSVe), Viale dell'Università, 10, 35020 Legnaro, Padova, Italy
5Lagoon Ecosystems UMR 5119, University of Montpellier 2, cc093, place E Bataillon, F-34095 Montpellier cedex 05, France
6Institute of Marine Research, CSIC, C/Eduardo Cabello, 6, E-36208 Vigo, Spain
7Department of Biology, University of Trieste, P.le Valmaura, 9, 34148 Trieste, Italy
corresponding authorCorresponding author.
#Contributed equally.
Paola Venier: paola.venier/at/unipd.it; Cristiano De Pittà: cristiano.depitta/at/unipd.it; Filippo Bernante: fbernante/at/cribi.unipd.it; Laura Varotto: lauravarotto/at/yahoo.it; Barbara De Nardi: barbara.denardi/at/entecra.it; Giuseppe Bovo: GBOVO/at/IZSVENEZIE.IT; Philippe Roch: philippe.roch/at/univ-montp2.fr; Beatriz Novoa: virus/at/iim.csic.es; Antonio Figueras: antoniofigueras/at/iim.csic.es; Alberto Pallavicini: pallavic/at/univ.trieste.it; Gerolamo Lanfranchi: gerolamo.lanfranchi/at/unipd.it
Received November 10, 2008; Accepted February 9, 2009.
Abstract
Background
Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.
Results
We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database http://mussel.cribi.unipd.it.
Conclusion
We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.
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