Comparative analysis of long non-coding RNAs in Atlantic and Coho salmon reveals divergent transcriptome responses associated with immunity and tissue repair during sea lice infestation. (October 2018)

• Record Type: Journal Article
• Authors: Valenzuela-Muñoz, Valentina; Valenzuela-Miranda, Diego; Gallardo-Escárate, Cristian
• Is Part Of: Developmental and comparative immunology. Volume 87(2018)
• Page Start: 36
• Page End: 50
• Publication Date: 2018-10
• Subjects: LncRNA -- Atlantic salmon -- Coho salmon -- C. rogercresseyi; Immunology -- Periodicals; Developmental immunology -- Periodicals; 616.079
• DOI: 10.1016/j.dci.2018.05.016
• Languages: English
• ISSNs: 0145-305X

Abstract

Abstract: The increasing capacity of transcriptomic analysis by high throughput sequencing has highlighted the presence of a large proportion of transcripts that do not encode proteins. In particular, long non-coding RNAs (lncRNAs) are sequences with low coding potential and conservation among species. Moreover, cumulative evidence has revealed important roles in post-transcriptional gene modulation in several taxa. In fish, the role of lncRNAs has been scarcely studied and even less so during the immune response against sea lice. In the present study we mined for lncRNAs in Atlantic salmon ( Salmo salar ) and Coho salmon ( Oncorhynkus kisutch ), which are affected by the sea louse Caligus rogercresseyi, evaluating the degree of sequence conservation between these two fish species and their putative roles during the infection process. Herein, Atlantic and Coho salmon were infected with 35 lice/fish and evaluated after 7 and 14 days post-infestation (dpi). For RNA sequencing, samples from skin and head kidney were collected. A total of 5658/4140 and 3678/2123 lncRNAs were identified in uninfected/infected Atlantic and Coho salmon transcriptomes, respectively. Species-specific transcription patterns were observed in exclusive lncRNAs according to the tissue analyzed. Furthermore, neighbor gene GO enrichment analysis of the top 100 highly regulated lncRNAs in Atlantic salmon showed that lncRNAs were localized near genes related to the immune response. On the other hand, in Coho salmon the highly regulated lncRNAs were localized near genes involved in tissue repair processes. This study revealed high regulation of lncRNAs closely localized to immune and tissue repair-related genes in Atlantic and Coho salmon, respectively, suggesting putative roles for lncRNAs in salmon against sea lice infestation . Highlights: LncRNAs were identified in infected Atlantic and Coho salmon transcriptomes. Atlantic and coho salmon showed tissue-specific lncRNAs transcription patterns. LncRNAs highly regulated in infected-Atlantic salmon were co-localized with immune-related genes. Coho salmon lncRNAs highly modulated were co-localized to tissue repair-related genes.