title: Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.
abstract: BACKGROUND
  The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1).
  
  
  RESULTS
  Sequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts.
  
  
  CONCLUSIONS
  The newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.
authors.affiliation: Nutrigenomics and Fish Growth Endocrinology Group, Department of Marine Species Biology, Culture and Pathology, Institute of Aquaculture Torre de la Sal, Castellón, CSIC, Spain.
authors.forename: Josep A
authors.initials: JA
authors.lastname: Calduch-Giner
authors.forename: Azucena
authors.initials: A
authors.lastname: Bermejo-Nogales
authors.forename: Laura
authors.initials: L
authors.lastname: Benedito-Palos
authors.forename: Itziar
authors.initials: I
authors.lastname: Estensoro
authors.forename: Gabriel
authors.initials: G
authors.lastname: Ballester-Lozano
authors.forename: Ariadna
authors.initials: A
authors.lastname: Sitjà-Bobadilla
authors.forename: Jaume
authors.initials: J
authors.lastname: Pérez-Sánchez
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D030562:Databases, Protein; D020869:Gene Expression Profiling; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics*; D012313:RNA / Q000235:genetics; D021541:Sea Bream / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012313:RNA