Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers

Louro, Bruno; Passos, Ana Lúcia S.; Souche, Erika L.; Tsigenopoulos, Costas; Beck, Alfred; Lagnel, Jacques; Bonhomme, François; Cancela, Leonor; Cerdà, Joan; Clark, Melody S. ORCID: https://orcid.org/0000-0002-3442-3824; Lubzens, Esther; Magoulas, Antonis; Planas, Josep V.; Volckaert, Filip A.M.; Reinhardt, Richard; Canario, Adelino V.M.. 2010 Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers. Marine Genomics, 3 (3-4). 179-191. 10.1016/j.margen.2010.09.005

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Abstract/Summary

The gilthead sea bream. Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 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, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value <10(-5)) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene 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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1016/j.margen.2010.09.005
Programmes:	BAS Programmes > Polar Science for Planet Earth (2009 - ) > Ecosystems
ISSN:	1874-7787
Additional Keywords:	Expressed Sequence Tag; microsatellite; single nucleotide polymorphism; annotation; aquaculture; teleost fish
NORA Subject Terms:	Marine Sciences Biology and Microbiology Data and Information
Date made live:	21 Jun 2011 13:28 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/14523

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1016/j.margen.2010.09.005

Programmes:

BAS Programmes > Polar Science for Planet Earth (2009 - ) > Ecosystems

ISSN:

1874-7787

Additional Keywords:

Expressed Sequence Tag; microsatellite; single nucleotide polymorphism; annotation; aquaculture; teleost fish

NORA Subject Terms:

Marine Sciences
Biology and Microbiology
Data and Information