Abstract
Bacterial cold-water disease caused by Flavobacterium psychrophilum is one of the major causes of mortality of salmonids. Three genetic lines of rainbow trout designated as ARS-Fp-R (resistant), ARS-Fp-C (control) and ARS-Fp-S (susceptible) have significant differences in survival rate following F. psychrophilum infection. Previous study identified transcriptome differences of immune-relevant protein-coding genes at basal and post infection levels among these genetic lines. Using RNA-Seq approach, we quantified differentially expressed (DE) long non-coding RNAs (lncRNAs) in response to F. psychrophilum challenge in these genetic lines. Pairwise comparison between genetic lines and different infection statuses identified 556 DE lncRNAs. A positive correlation existed between the number of the differentially regulated lncRNAs and that of the protein-coding genes. Several lncRNAs showed strong positive and negative expression correlation with their overlapped, neighboring and distant immune related protein-coding genes including complement components, cytokines, chemokines and several signaling molecules involved in immunity. The correlated expressions and genome-wide co-localization suggested that some lncRNAs may be involved in regulating immune-relevant protein-coding genes. This study provides the first evidence of lncRNA-mediated regulation of the anti-bacterial immune response in a commercially important aquaculture species and will likely help developing new genetic markers for rainbow trout disease resistance.
Highlights
Compared to a susceptible (ARS-Flavobacterium psychrophilum (Fp)-S) and randomly bred control (ARS-Fp-C) lines[8]
On average, 8.2% of the total RNA-Seq reads aligned to the 31,195 lncRNAs reference (Supplementary Dataset 1A). 94.5% of the reads were uniquely mapped to the reference
RNA was sequenced from a whole-body extract, which may be another reason for the low percentage of mappable reads because reference lncRNA dataset was sequenced from about 13 specific tissues
Summary
Compared to a susceptible (ARS-Fp-S) and randomly bred control (ARS-Fp-C) lines[8]. Previously, we performed global expression analysis of protein-coding genes in these genetic lines upon Fp challenge[9]. To the best of our knowledge, there are no studies exploring the expression of lncRNAs during host defense against bacterial infection in aquaculture finfish. Such studies are difficult as low evolutionary conservation of lncRNAs across species prevents utilization of the information from mammalian species into aquaculture animals. The overall objective of this study was to identify lncRNAs that are associated with genetic resistance against Fp and to identify immune-relevant protein-coding genes that might be regulated by lncRNAs. To study the expression of lncRNA, we utilized a reference dataset that we recently identified (31,195 lncRNA) in rainbow trout[20]. We have identified DE lncRNAs between genetic lines of naive animals and in response to infection, identified their genomic co-localization relative to immune-relevant protein-coding genes, and explored their co-expression relationships to suggest possible regulation of immune-relevant protein-coding genes by lncRNAs
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