Abstract
Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection.
Highlights
Despite evidence for participation in the host response to infection, the roles of many long non-coding
Analysis of a subset of these lncRNAs showed the following: (i) Most were regulated in response to Infectious salmon anemia (ISA) virus infection; (ii) The transcript subsets were uniquely modulated in each tissue; and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection
The results showed a widespread differentiation of lncRNAs in response to ISAV infection, suggesting that these transcripts are involved in regulating the host response to the virus
Summary
Despite evidence for participation in the host response to infection, the roles of many long non-coding. Analysis of a subset of these lncRNAs showed the following: (i) Most were regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection. These include H19, which is the precursor of miR-675, a moderator of cell growth[11]; and MALAT1, which forms a molecular scaffold for several proteins present in nuclear speckles and which regulates pre-mRNA alternative splicing[12]
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