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.

Long noncoding RNAs: Unexplored players in the drug response of the sea louse Caligus rogercresseyi

“…However, lncRNA research in marine species is still limited and has been mainly associated with functions in immune responses (Boltaña et al, 2016;Mu et al, 2016;Paneru et al, 2016). Therefore, our work aimed to identify lncRNAs in the sea louse C. rogercresseyi and to evaluate the transcriptional modulation of these during exposure to the delousing drugs deltamethrin and azamethiphos.…”

“…closely related species has been reported (Pauli et al, 2012;Etebari et al, 2015;Mu et al, 2016;Paneru et al, 2016).…”

“…Furthermore, cumulative evidence suggests little sequence conservation between lncRNAs, even in closely related species (Pauli et al, 2012;Etebari et al, 2015;Paneru et al, 2016). This has hampered the identification of lncRNAs in non-model species, and, hence, the characterization of lncRNAs relies on the removal of transcripts evidencing coding potential.…”

“…Considering the emerging evidence suggesting the importance of lncRNAs in the regulation of diverse biological process, together with the limited data regarding lncRNAs in marine species (Gaiti et al, 2015;Boltaña et al, 2016;Mu et al, 2016;Paneru et al, 2016), the present study focused on identifying lncRNAs in C. rogercresseyi and evaluating transcriptional modulation during exposure to the delousing drugs deltamethrin and azamethiphos. Through a custom pipeline, 1835 putative lncRNAs were identified that shared features classical of other previously reported lncRNAs.…”

Marine Environmental Epigenetics

“…Accordingly, gene regulation mediated by ncRNAs has been linked to development, sex determination, and reproduction in oysters (Yu et al 2016) and teleost fishes (Bizuayehu et al 2012a(Bizuayehu et al ,b, 2015Cochrane et al 2011, Mennigen et al 2013, Robledo et al 2017. A role for ncRNAs was also proposed during environmental responses to stress in marine organisms, including responses to virus and bacterial infection in Atlantic salmon (Boltaña et al 2016) and rainbow trout (Paneru et al 2016). miRNA participation during responses to thermal stress has also been identified in Atlantic cod, although a study of DNA methylation in the promoters of differentially expressed miRNAs had inconclusive results (Bizuayehu et al 2015).…”