Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform
<p>Abstract</p> <p>Background</p> <p>The Senegalese sole, <it>Solea senegalensis</it>, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/508 |
| _version_ | 1811281564262203392 |
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| author | Planas Josep V Piferrer Francesc Martínez-Rodríguez Gonzalo Cañavate Pedro Asensio Esther Castellana Barbara Viñas Jordi Halm Silke Infante Carlos Astola Antonio Tingaud-Sequeira Angèle Manchado Manuel Mercadé Jaume Lozano Juan Cerdà Joan Prat Francesc Yúfera Manuel Durany Olga Subirada Francesc Rosell Elisabet Maes Tamara |
| author_facet | Planas Josep V Piferrer Francesc Martínez-Rodríguez Gonzalo Cañavate Pedro Asensio Esther Castellana Barbara Viñas Jordi Halm Silke Infante Carlos Astola Antonio Tingaud-Sequeira Angèle Manchado Manuel Mercadé Jaume Lozano Juan Cerdà Joan Prat Francesc Yúfera Manuel Durany Olga Subirada Francesc Rosell Elisabet Maes Tamara |
| author_sort | Planas Josep V |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The Senegalese sole, <it>Solea senegalensis</it>, 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.</p> <p>Results</p> <p>Sequencing of a <it>S. senegalensis </it>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.</p> <p>Conclusion</p> <p>New genomic resources have been developed for <it>S. senegalensis</it>, 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.</p> |
| first_indexed | 2024-04-13T01:35:52Z |
| format | Article |
| id | doaj.art-eb9d510286d748b8ba3588e2449925d9 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T01:35:52Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-eb9d510286d748b8ba3588e2449925d92022-12-22T03:08:24ZengBMCBMC Genomics1471-21642008-10-019150810.1186/1471-2164-9-508Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platformPlanas Josep VPiferrer FrancescMartínez-Rodríguez GonzaloCañavate PedroAsensio EstherCastellana BarbaraViñas JordiHalm SilkeInfante CarlosAstola AntonioTingaud-Sequeira AngèleManchado ManuelMercadé JaumeLozano JuanCerdà JoanPrat FrancescYúfera ManuelDurany OlgaSubirada FrancescRosell ElisabetMaes Tamara<p>Abstract</p> <p>Background</p> <p>The Senegalese sole, <it>Solea senegalensis</it>, 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.</p> <p>Results</p> <p>Sequencing of a <it>S. senegalensis </it>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.</p> <p>Conclusion</p> <p>New genomic resources have been developed for <it>S. senegalensis</it>, 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.</p>http://www.biomedcentral.com/1471-2164/9/508 |
| spellingShingle | Planas Josep V Piferrer Francesc Martínez-Rodríguez Gonzalo Cañavate Pedro Asensio Esther Castellana Barbara Viñas Jordi Halm Silke Infante Carlos Astola Antonio Tingaud-Sequeira Angèle Manchado Manuel Mercadé Jaume Lozano Juan Cerdà Joan Prat Francesc Yúfera Manuel Durany Olga Subirada Francesc Rosell Elisabet Maes Tamara Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform BMC Genomics |
| title | Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform |
| title_full | Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform |
| title_fullStr | Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform |
| title_full_unstemmed | Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform |
| title_short | Genomic resources for a commercial flatfish, the Senegalese sole (<it>Solea senegalensis</it>): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform |
| title_sort | genomic resources for a commercial flatfish the senegalese sole it solea senegalensis it est sequencing oligo microarray design and development of the soleamold bioinformatic platform |
| url | http://www.biomedcentral.com/1471-2164/9/508 |
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