title: Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform.
abstract: BACKGROUND
  The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species.
  
  
  RESULTS
  Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data.
  
  
  CONCLUSIONS
  New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.
authors.affiliation: Laboratory of the Institut de Recerca i Tecnologia Agroalimentàries-Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, 08003 Barcelona, Spain. joan.cerda@irta.es
authors.forename: Joan
authors.initials: J
authors.lastname: Cerdà
authors.forename: Jaume
authors.initials: J
authors.lastname: Mercadé
authors.forename: Juan José
authors.initials: JJ
authors.lastname: Lozano
authors.forename: Manuel
authors.initials: M
authors.lastname: Manchado
authors.forename: Angèle
authors.initials: A
authors.lastname: Tingaud-Sequeira
authors.forename: Antonio
authors.initials: A
authors.lastname: Astola
authors.forename: Carlos
authors.initials: C
authors.lastname: Infante
authors.forename: Silke
authors.initials: S
authors.lastname: Halm
authors.forename: Jordi
authors.initials: J
authors.lastname: Viñas
authors.forename: Barbara
authors.initials: B
authors.lastname: Castellana
authors.forename: Esther
authors.initials: E
authors.lastname: Asensio
authors.forename: Pedro
authors.initials: P
authors.lastname: Cañavate
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Martínez-Rodríguez
authors.forename: Francesc
authors.initials: F
authors.lastname: Piferrer
authors.forename: Josep V
authors.initials: JV
authors.lastname: Planas
authors.forename: Francesc
authors.initials: F
authors.lastname: Prat
authors.forename: Manuel
authors.initials: M
authors.lastname: Yúfera
authors.forename: Olga
authors.initials: O
authors.lastname: Durany
authors.forename: Francesc
authors.initials: F
authors.lastname: Subirada
authors.forename: Elisabet
authors.initials: E
authors.lastname: Rosell
authors.forename: Tamara
authors.initials: T
authors.lastname: Maes
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D020224:Expressed Sequence Tags; D005412:Flatfishes / Q000235:genetics*; D015723:Gene Library; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods