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Expressed Sequence Tags: Characterization, Tissue-Specific Expression and Gene Markers

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Expressed Sequence Tags: Characterization, Tissue-Specific Expression and Gene Markers Marine Genomics 3 (2010) 179–191 Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers Bruno Louro a,j, Ana Lúcia S. Passos a, Erika L. Souche b,1, Costas Tsigenopoulos c, Alfred Beck d, Jacques Lagnel c, François Bonhomme e, Leonor Cancela a, Joan Cerdà f, Melody S. Clark g, Esther Lubzens h, Antonis Magoulas c, Josep V. Planas i, Filip A.M. Volckaert b, Richard Reinhardt d, Adelino V.M. Canario a,⁎ a Centre of Marine Sciences, University of Algarve, Building 7, Gambelas, 8000-139 Faro, Portugal b Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium c Hellenic Centre for Marine Research, Institute of Marine Biology and Genetics, Thalassocosmos, Ex-US base at Gournes, P.O. Box 2214, Gournes Pediados, 715 00 Heraklion, Crete, Greece d MPI Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany e Département Biologie Intégrative, Institut des Sciences de l'Evolution, UMR 5554 Université de Montpellier 2, cc 63 — Pl. E Bataillon, F34095 Montpellier Cedex 5, France f Laboratory of Institut de Recerca i Tecnologia Agroalimentaries (IRTA)-Institut de Ciencies del Mar (Consejo Superior de Investigaciones Científicas, CSIC), Passeig Marítim 37-49, 08003-Barcelona, Spain g British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK h National Institute of Oceanography, Israel Oceanographic & Limnological Research, P.O. Box 8030, Haifa 31080, Israel i Departament de Fisiologia, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain j Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Roslin, Midlothian, EH25 9PS, United Kingdom article info abstract Article history: The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most Received 16 May 2010 important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for Received in revised form 17 September 2010 the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 Accepted 21 September 2010 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, Keywords: representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea Expressed Sequence Tag fi Microsatellite bass, sea bream and in the model sh Gasterosteus aculeatus genomes, it was estimated that approximately Single nucleotide polymorphism two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST − Annotation sequence similarity searches (using a cut off of e-value b10 5) against fully the curated SwissProt (and Aquaculture TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene Teleost fish datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog's for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species. © 2010 Elsevier B.V. All rights reserved. ⁎ Corresponding author. E-mail addresses: [email protected] (B. Louro), [email protected] (A.L.S. Passos), [email protected] (E.L. Souche), [email protected] (C. Tsigenopoulos), [email protected] (A. Beck), [email protected] (J. Lagnel), [email protected] (F. Bonhomme), [email protected] (L. Cancela), [email protected] (J. Cerdà), [email protected] (M.S. Clark), [email protected] (E. Lubzens), [email protected] (A. Magoulas), [email protected] (J.V. Planas), [email protected] (F.A.M. Volckaert), [email protected] (R. Reinhardt), [email protected] (A.V.M. Canario). 1 Current address: Institut Pasteur, Plate-Forme Intégration et Analyse Génomiques, 28 Rue du Docteur Roux, F-75724 Paris Cedex 15, France. 1874-7787/$ – see front matter © 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.margen.2010.09.005 180 B. Louro et al. / Marine Genomics 3 (2010) 179–191 1. Introduction assembly and annotation of draft genome sequence (Kuhl et al., 2010)], sea bass radiation hybrid map and QTL mapping (Massault et The gilthead sea bream, Sparus auratus, and the European sea bass, al., 2010). Dicentrarchus labrax, are two of the main marine fish species cultured in Southern Europe. Both species are economically valuable and, therefore, 2. Methods over the last two decades efforts have been made to increase the knowledge of their physiology, reproduction, immunology, ecology, 2.1. cDNA libraries construction quantitative genetics and population genetics (Power et al., 2001; Scapigliati et al., 2002; Piferrer et al., 2005; Pawson et al., 2007; Lemaire The sea bream and sea bass were obtained from local fish farms and et al., 2005; Laiz-Carrion et al., 2005; Arends et al., 1999; Senger et al., maintained at the Ramalhete marine station (University of Algarve, 2006; Meiri et al., 2002). The fact that these are not designated model Faro, Portugal). The sea bream cDNA libraries were made from tissue fish species has contributed to the shortage of genomic resources. pools of 9 animals, ranging in weight between 0.3 and 4 kg and However, recently there has been growing awareness of the value of included males (2), females (4) and hermaphrodites (3). The sea bass genomic information in the efficient implementation of strategies for cDNA libraries were made from tissue pools from 5 male individuals of selective breeding, disease prevention, treatment and quality control in approximately 450 g except for the ovarian tissue which came from a cultured fish species. Therefore, the EU Network of Excellence Marine single individual from a separate stock. Animals were sacrificed with Genomics Europe (MGE; http://www.marine-genomics-europe.org/) an excess of 2-phenoxyethanol, tissues were dissected and stored in set out to develop EST (expressed sequence tags; single-pass sequencing liquid nitrogen at −80°C. Total RNA was extracted using the acid of cDNA libraries) projects on aquacultured marine fish species, focusing guanidinium thiocyanate-phenol-chloroform method (Chomczynski on the sea bream and the sea bass. These EST projects represent an and Sacchi, 1987). important contribution to the genomic resources of these two species. Fourteen normalized tissue-specific cDNA libraries were con- The generation and analysis of ESTs is a valuable approach for the structed and normalized from liver; ovary; testis; bone/cartilage; identification and characterization of new genes and provide a platform brain/pituitary; heart/vessels; adipose; head/kidney; trunk/kidney; for developing functional genomics methods (Gong, 1999; Douglas gill; intestine; spleen; muscle; and skin of each species. cDNA library et al., 1999; 2007; Gonzalez et al., 2007; Cerdà et al., 2008; Canario et al., construction and sequencing was carried out at the Max Planck 2008; Koop et al., 2008). Institute of Molecular Genetics (Berlin, Germany). mRNA purifications Representation of transcript abundance and diversity in EST and concentration were performed using the Dynal's oligo-dT collections is dependent on the method of cDNA library construction. magnetic beads (Invitrogen Dynal AS, Olso, Norway). cDNA libraries If the objective is to obtain the widest possible representation of cDNAs, were constructed using the cDNA SMART-kit (Clontech, Palo Alto, CA, then it is a common procedure to normalize the cDNA libraries prior to USA) (Zhu et al., 2001) and normalized using thermostable duplex- sequencing in order to increase the presence of rare transcripts, specific nuclease (Zhulidov et al., 2004). however the gene expression profiles are lost (Bonaldo et al., 1996; Coblentz et al., 2006; Govoroun et al., 2006). In contrast, non normalized 2.2. Sequencing: editing and cluster assembly cDNA libraries may be deficient in rare transcripts, unless deep sequencing coverage is achieved, something that is now more accessible Sequencing was performed using Capillary Sequencer systems (ABI with Next Generation pyrosequencing (Morozova and Marra, 2008). 3730 XL and GE Healthcare MegaBace 4500) at the Max Planck Institute Fish EST projects started
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