Differential expression of long non-coding RNAs in three genetic lines of rainbow trout (Oncorhynchus mykiss) in response to infection with Flavobacterium psychrophilum

Authors: PANERU, BAM - Middle Tennessee State University; AL TOBASEI, RAFET - Middle Tennessee State University; Palti, Yniv; Wiens, Gregory - Greg; SALEM, MOHAMED - Middle Tennessee State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2016
Publication Date: 10/27/2016
Citation: Paneru, B., Al Tobasei, R., Palti, Y., Wiens, G.D., Salem, M. 2016. Differential expression of long non-coding RNAs in three genetic lines of rainbow trout (Oncorhynchus mykiss) in response to infection with Flavobacterium psychrophilum. Scientific Reports. 6:36032 doi: 10.1038/srep36032.

Interpretive Summary: Selective breeding for disease resistance offers new opportunities for improving fish welfare in aquaculture. At our location, we have produced a line of rainbow trout that has increased resistance against Flavobacterium psychrophilum, the cause of bacterial cold water disease (BCWD). The mechanisms governing disease resistance are unknown. In a previous study, we analyzed gene expression of protein coding genes in disease resistant, disease susceptible, and control fish after one day and five days after infection with F. psychrophilum. In this study, we reanalyzed the same dataset for changes in expression of long non-coding RNAs (lncRNA). LncRNA are non-protein coding transcripts longer than 200 nucleotides. The function of LncRNAs is poorly understood, but in many cases they are involved in regulating protein coding genes. We describe the identification of over 500 of lncRNAs that have different levels of abundance between the three genetic lines of fish. These genes may be influenced by selective breeding and play a role in survival. This study is important because it characterizes the fish response to infection on a genetic level, demonstrates quantifiable differences between selectively bred fish lines, and suggests immune and physiologic mechanisms associated with survival.

Technical 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 immunerelevant 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.