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oai:recercat.cat:20.500.12327/36532025-10-22T11:01:12Zcom_2072_4428com_2072_4427col_2072_487898

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform Cerdà Luque, Joan Mercadé, Jaume Lozano, Juan José Manchado, Manuel Sequeira, Angela Astola, Antonio Infante, Carlos Halm, Silke Viñas, Jordi Castellana, Barbara Asensio, Esther Cañavate, Pedro Martínez-Rodríguez, Gonzalo Piferrer, Francesc Planas, Josep V Prat, Francesc Yúfera, Manuel Durany, Olga Subirada, Francesc Rosell, Elisabet Maes, Tamara Producció Animal Aqüicultura 575 637 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. This research was supported by Genome Spain and Genome Canada within the framework of the international consortium Pleurogene™. We thank J. L. Gelpí and Dmitry Repchevsky for technical assistance to install the Soleamold software in the website of the Spanish National Institute of Bioinformatics info:eu-repo/semantics/publishedVersion 2008-10-30 info:eu-repo/semantics/article Cerda, Joan, Jaume Mercade, Juan Jose Lozano, Manuel Manchado, Angele Tingaud-Sequeira, Antonio Astola, Carlos Infante, et al. 2008. “Genomic Resources for a Commercial Flatfish, the Senegalese Sole (Solea Senegalensis): EST Sequencing, Oligo Microarray Design, and Development of the Bioinformatic Platform Soleamold.” BMC Genomics 9 (1): 508. doi: 10.1186/1471-2164-9-508 1471-2164 http://hdl.handle.net/20.500.12327/3653 https://doi.org/10.1186/1471-2164-9-508 eng BMC Genomics Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess 14 BioMed Central