Analysis of gene expression in nodavirus-inoculated Senegalese sole using a new Openarray® platform.

Abstract

Nervous necrosis virus (NNV) is the causative agent of the viral encephalopathy and retinopathy, a disease that affects cultured Senegalese sole (Solea senegalensis). A NNV reassortant (Ss160.03), combining genomic segments from red-spotted grouper nervous necrosis virus (RGNNV) and striped jack nervous necrosis virus (SJNNV) genotypes, has been previously isolated from Senegalese sole, being highly virulent to this fish species. The RNA-Seq technology has been used in a previous study to comparatively analyse Senegalese sole transcriptomes in two organs (head kidney and eye/brain) after infection with two NNV virus with different levels of virulence to that fish species, a highly virulent reassortant isolate (wSs160.03) and a less virulent mutant reassortant obtained by reverse genetics (rSs160.03247þ270). To validate previous RNA-Seq results, a 112- assay OpenArray® platform (Thermofisher) has been designed. This platform included 89 genes chosen according to transcriptomic changes observed by RNA-Seq (covering PRRs, type I IFN response, signal transduction, inflammation, virus responsive genes, and apoptosis), 17 genes selected based on their previously described relation with the immune response against fish viral infections, and 6 control genes (including 3 endogenous genes and 3 viral genes).