title: Differential expression of long non-coding RNAs in three genetic lines of rainbow trout in response to infection with Flavobacterium psychrophilum.
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.
authors: Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, U.S.
authors: Bam
authors: B
authors: Paneru
authors: Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, U.S.
authors: Rafet
authors: R
authors: Al-Tobasei
authors: The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV 25430, U.S.
authors: Yniv
authors: Y
authors: Palti
authors: The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV 25430, U.S.
authors: Gregory D
authors: GD
authors: Wiens
authors: Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, U.S.|Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, U.S.
authors: Mohamed
authors: M
authors: Salem
mesh_terms: D000818:Animals; D005393:Fish Diseases / Q000276:immunology* / Q000382:microbiology*; D045826:Flavobacteriaceae Infections / Q000276:immunology / Q000662:veterinary*; D005417:Flavobacterium / Q000276:immunology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D054884:Host-Pathogen Interactions; D017686:Oncorhynchus mykiss; D062085:RNA, Long Noncoding / Q000096:biosynthesis* / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding