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

Overview
TitleComparative 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
AuthorsValenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C
TypeJournal Article
Journal NameDevelopmental and comparative immunology
VolumeN/A
IssueN/A
Year2018
Page(s)N/A
CitationValenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C. 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. Developmental and comparative immunology. 2018 May 24.

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.

Properties
Additional details for this publication include:
Property NameValue
Journal CountryUnited States
Publication TypeJournal Article
Language Abbreng
LanguageEnglish
CopyrightCopyright © 2018. Published by Elsevier Ltd.
DOI10.1016/j.dci.2018.05.016
Elocation10.1016/j.dci.2018.05.016
PIIS0145-305X(18)30031-4
Journal AbbreviationDev. Comp. Immunol.
Publication Date2018 May 24
eISSN1879-0089
ISSN1879-0089
Publication ModelPrint-Electronic
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DatabaseAccession
PMID: PMID:29803715