Abstract
Long noncoding RNAs (lncRNAs) are being increasingly recognised as key modulators of various biological mechanisms, including the immune response. Although investigations in teleosts are still lagging behind those conducted in mammals, current research indicates that lncRNAs play a pivotal role in the response of fish to a variety of pathogens. During the last several years, interest in lncRNAs has increased considerably, and a small but notable number of publications have reported the modulation of the lncRNA profile in some fish species after pathogen challenge. This study was the first to identify lncRNAs in the commercial species European sea bass. A total of 12,158 potential lncRNAs were detected in the head kidney and brain. We found that some lncRNAs were not common for both tissues, and these lncRNAs were located near coding genes that are primarily involved in tissue-specific processes, reflecting a degree of cellular specialisation in the synthesis of lncRNAs. Moreover, lncRNA modulation was analysed in both tissues at 24 and 72 h after infection with nodavirus. Enrichment analysis of the neighbouring coding genes of the modulated lncRNAs revealed many terms related to the immune response and viral infectivity but also related to the stress response. An integrated analysis of the lncRNAs and coding genes showed a strong correlation between the expression of the lncRNAs and their flanking coding genes. Our study represents the first systematic identification of lncRNAs in European sea bass and provides evidence regarding the involvement of these lncRNAs in the response to nodavirus.
Highlights
European sea bass (Dicentrarchus labrax L.) is a very valuable fish species, especially for Mediterranean countries
680 million reads were obtained from the different samples of European sea bass with an average of 28 million per sample, and over 99% of raw reads met the quality control standards
In a previous analysis of the coding transcriptome, we found a strong regulation of genes in calcium homeostasis in the brain, and the concentration of this cation seems to be highly altered involved in calcium homeostasis in the brain, and the concentration of this cation seems to be highly during nervous necrosis virus (NNV) infection and is crucial for infectivity [15]
Summary
European sea bass (Dicentrarchus labrax L.) is a very valuable fish species, especially for Mediterranean countries. Different diseases cause important economic losses and represent a major limiting factor for production These effects are observed for nervous necrosis virus (NNV), or nodavirus, a member of the family Nodaviridae, genus Betanodavirus, which can affect numerous aquatic animals, including a wide variety of marine and freshwater fish species [2]. This icosahedral, nonenveloped, positive-sense single-stranded RNA virus is the causative agent of viral encephalopathy and retinopathy (VER), which is characterised by damage to its target tissues, Biology 2020, 9, 165; doi:10.3390/biology9070165 www.mdpi.com/journal/biology. Among the four nodavirus genotypes, European sea bass seems to be primarily affected by red-spotted grouper nervous necrosis virus (RGNNV), especially during larval and juvenile stages [2,3]
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