Abstract
MicroRNAs (miRNAs) are small non-coding RNAs capable of altering gene expression. In viruses, miRNAs may significantly influence the interaction between the virus and its host. Among all the viruses that have been reported to encode miRNAs, those belonging to the Herpesvirales order encode the largest number of pre-miRNAs. Cyvirus cyprinidallo3 (CyHV-3) is a member of the Alloherpesviridae family and is recognised as a significant threat for the common carp and ornamental koi aquaculture. The present study aimed to identify miRNAs involved in the lytic cycle of CyHV-3 and monitor their expression from 1 h to 10 days post-infection (dpi), at two different temperatures: a permissive temperature (22 °C) and a non-permissive temperature (30 °C) (Fig. 1). This is the first study that describes the expression kinetics of predicted miRNAs from CyHV-3-infected carp cells. Alignment of reads against a CyHV-3 reference genome led to the identification of 81 putative pre-miRNAs. Although this data mainly focused on CyHV-3 miRNAs, an alignment of reads against the Cyprinus carpio genome led to the identification of 3025 miRNA that could be annotated. Of note, the 7 miRNAs previously identified in CyHV-3 were retrieved among the 81 putative pre-miRNAs found here. The number of putative miRNAs identified is far higher than in the two previous studies, probably because of the high number of reads obtained across the 36 individual samples that represented all stages of viral infection. A constant increase in the expression of virus-predicted miRNAs was observed along the viral infection at 22 °C, with a maximum at 6 dpi (Fig. 2). Interestingly, cytopathic effects started to be observed after 3 dpi, and all the cells were lysed after 10 days. In contrast, no cyctopathic effects were recorded at 30 °C; at this temperature, no difference could be observed between samples in terms of miRNA expression (Fig. 2).