Gene Expression Profiles of Spleen, Liver, and Head Kidney in Turbot (Scophthalmus maximus) Along the Infection Process with Philasterides dicentrarchi Using an Immune-Enriched Oligo-Microarray

Abstract

We evaluated the expression profiles of turbot in spleen, liver, and head kidney across five temporal points of the Philasterides dicentrarchi infection process using an 8x15K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify 221 differentially expressed (DE) genes (8.1% of the whole microarray), 113 in spleen, 83 in liver, and 90 in head kidney, in at least 1 of the 5 temporal points sampled for each organ. Most of these genes could be annotated (83.0%) and functionally categorized using GO terms (69.1%) after the additional sequencing of DE genes from the 5' end. Many DE genes were related to innate and acquired immune functions. A high proportion of DE genes were organ-specific (70.6%), although their associated GO functions showed notable similarities in the three organs. The most striking difference in functional distribution was observed between the up- and downregulated gene groups. Upregulated genes were mostly associated to immune functions, while downregulated ones mainly involved metabolism-related genes. Genetic response appeared clustered in a few groups of genes with similar expression profiles along the temporal series. The information obtained will aid to understand the turbot immune response and will specifically be valuable to develop strategies of defense to P. dicentrarchi to achieve more resistant broodstocks for turbot industry.

Vaccine-induced modulation of gene expression in turbot peritoneal cells. A microarray approach

“…Elongation factor 1-alpha, the selected housekeeping gene, showed very low variation across the experimental conditions tested (CV: 0.026). We found a high correlation between Q-PCR and microarray expression values (Pearson coefficient = 0.78; P = 0), indicating the consistency of our microarray data, as found in previous studies in turbot (Millan et al, 2010(Millan et al, , 2011Pardo et al, 2012).…”

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

“…Therefore, the first Turbot database was originally created with almost ten thousand high-quality ESTs sequences [36] (Table 1). From this database, a first custom oligo-microarray (8X15 Agilent) was successfully designed [37] and applied for evaluating expression profiles of genes involved in defense against pathogens [38,39]. …”

Genomics advances for boosting aquaculture breeding programs in Spain

“…Microsatellites were used both to organize broodstock according to minimum parentage (relatedness or inbreeding estimators), to allocate parents and estimate breeding values in competing mixing families (paternity analysis), and also to check the goodness of families founded in breeding programs (Castro et al, 2004). Molecular traceability tools have been later Millán et al, 2011;Díaz-Rosales et al, 2012;Pardo et al, 2012;Ribas et al, 2016). A similar pathway regarding transcriptome databases and microarray design was followed later for sea bass (Louro et al, 2010) and sea bream (Calduch-Giner et al, 2010, and for mollusks such as Manila clam (Moreira et al, 2012(Moreira et al, , 2014Romero et al, 2015) and European flat oyster .…”

“…QTL for sex determination (Martínez et al, 2009; Taboada et al, 2014b), growth rate (Sánchez-Molano et al, 2011), and resistance to the main turbot pathogens, the bacterium Aeromonas salmonicida (Rodríguez-Ramilo et al, 2011), the parasite Philasterides dicentrarchi (Rodríguez-Ramilo et al, 2013) and the hemorrhagic (VHS; Rodríguez-Ramilo et al, 2014) were identified. The last most prominent achievement in this species has been the whole genome sequencing (Figueraset al, 2016), which is being used as reference for gene expression analysis(Robledo et al, 2014;Ronza et al, 2016), high-throughput marker development for population screening (AQUATRACE EU project 311920), genomic selection (FISHBOOST EU project 613611), and gene mining(Bouza et al, 2012). The results of these studies are being applied in marker assisted selection (MAS) programs by turbot industry to obtain all-female populations, and a set of suitable markers have been identified for MAS programs to increase growth rate(Sciara et al, 2015).…”

“…Anonymous microsatellites were used to construct the turbot genetic map(Bouza et al, 2007), the first of the Spanish Science on this field, and to locate centromeres using half-tetrads using diploid gynogenetic families(Martínez et al, 2008). Later, gene-associated markers (SNPs and microsatellites) were used to enrich the turbot map (~500 markers;Bouza et al, 2008Bouza et al, , 2012 and BAC clones were applied as FISH probes to establish the correspondence between the cytogenetic and the geneticmaps (Taboada et al, 2014a). The turbot map has been profusely applied to detect quantitative trait loci (QTL) for the most relevant industrial traits and to identify candidate genes responsible of the associations detected through comparative genomics with model fish.…”