Open Access Research article

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

Joan Cerdà1*, Jaume Mercadé2, Juan José Lozano3, Manuel Manchado4, Angèle Tingaud-Sequeira1, Antonio Astola5, Carlos Infante4, Silke Halm5, Jordi Viñas6, Barbara Castellana7, Esther Asensio4, Pedro Cañavate4, Gonzalo Martínez-Rodríguez5, Francesc Piferrer6, Josep V Planas7, Francesc Prat5, Manuel Yúfera5, Olga Durany2, Francesc Subirada2, Elisabet Rosell2 and Tamara Maes2

Author Affiliations

1 Laboratory of the Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain

2 Oryzon Genomics, Scientific Parc University of Barcelona, 08028 Barcelona, Spain

3 CIBERehd, Hospital Clínic, 08036 Barcelona, Spain

4 IFAPA Centro "El Toruño", Junta de Andalucía, 11500 El Puerto de Santa María, Cádiz, Spain

5 Instituto de Ciencias Marinas de Andalucía, CSIC, 11510 Puerto Real, Cadiz, Spain

6 Institut de Ciències del Mar, CSIC, 08003 Barcelona, Spain

7 Department of Physiology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain

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BMC Genomics 2008, 9:508  doi:10.1186/1471-2164-9-508

Published: 30 October 2008

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.

Conclusion

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.