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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #324466

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Role of long non-coding RNAs in bacterial cold water disease pathogenesis in rainbow trout

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

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 12/29/2015
Publication Date: 1/9/2016
Citation: Paneru, B., Tobasei, R., Palti, Y., Wiens, G.D., Salem, M. 2016. Role of long non-coding RNAs in bacterial cold water disease pathogenesis in rainbow trout. Plant and Animal Genome. Paper No. 2-105.

Interpretive Summary:

Technical Abstract: Bacterial cold water disease (BCWD) caused by Flavobacterium psychrophilum is one of the major causes of mortality in 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 studies have identified transcriptome differences of immune-relevant protein-coding genes at basal and post-infection levels among these genetic lines. Using an RNA-seq approach, we quantified differentially expressed long non-coding RNAs (lncRNAs) in response to F. psychrophilum challenge. Pairwise comparison between genetic lines and different infection status identified 705 differentially expressed lncRNAs. A positive correlation was observed between the number of the differentially regulated lncRNAs and that of the protein-coding genes following infection. Many of the differentially expressed lncRNAs had genomic locations near immune-related protein-coding loci. Several lncRNAs showed strong correlation in expression patterns with their neighboring and distant immune related protein-coding genes. The list includes complement components, suppressor of cytokine signaling, tumor necrosis factor receptor superfamily members, chemokines, and transcription factor involved in immunological responsiveness. Most of the proteins coding genes that correlated in expression with lncRNAs were transcription factors, activators, receptors, and molecules of signal transduction pathways related to the innate immune system. The correlated expression 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 correlation of lncRNAs with immune related protein-coding genes in a commercially important aquaculture species and will likely help developing new genetic markers for fish disease resistance.