Modulation of Atlantic salmon miRNome response to sea louse infestation

Abstract

MicroRNAs are non-coding RNA that plays a crucial role in post-transcriptional regulation and immune system regulation. On other hand, sea lice are prevalent parasites that affect salmon farming, generating different degrees of immune suppression depending on the salmon and sea louse species. Caligus rogercresseyi for example, which affects the salmon industry in Chile, decreases Th1 response, macrophage activation, TLR-mediated response and iron regulation in infected fish. In this study, we explore Atlantic salmon miRNome during infestation by C. rogercresseyi. Using small RNA sequencing, we annotated 1718 miRNAs for skin and head kidney from infected Atlantic salmon. The most abundant families identified were mir-10, mir-21, mir-30, mir-181 and let7. Significant differences were found between tissue, with 1404 annotated miRNA in head kidney and 529 in skin. Differential analysis of transcript expression indicated that at an early stage of infestation miRNA expression was higher in head kidney than in skin tissue, revealing tissue-specific expression patterns. In parallel, miRNA target prediction using 3'UTRs from highly regulated immune-related genes and iron metabolism showed that mir-140-4 and mir-181a-2-5 modulate the expression of TLR22 and Aminolevulinic acid synthase, respectively. This study contributes knowledge about the immune response of Atlantic salmon during infestation with sea lice.

Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon

“…The dataset adds to the increasing volume of RNA-Seq information being made available by the research community. The majority of existing Atlantic salmon RNA-Seq datasets have been generated to address specific biological questions, including host response to disease challenge (Dettleff et al, 2017 ; Valenzuela-Muñoz et al, 2017 ; Rozas-Serri et al, 2018 ), developmental progression (Wang et al, 2014 ) or nutritional requirements (Jin et al, 2018 ). The consequence is a paucity of transcriptomic profiling of animals not subject to an experimental regime designed to elicit specific responses or that characterize a biological extreme.…”

The race between host and sea lice in the Chilean salmon farming: a genomic approach

“…From the transcriptome of Atlantic and Coho salmon infected with C. rogercresseyi , a high number of transcripts associated with iron modulation was observed from a GO enrichment analysis (Valenzuela‐Muñoz et al . ,). Furthermore, Atlantic salmon exhibit a high number of transcripts with functions including ion binding, ferric ion binding and ferrous ion binding, processes that were not observed in Coho salmon after infestation (Valenzuela‐Muñoz et al .…”

“…Furthermore, Atlantic salmon exhibit a high number of transcripts with functions including ion binding, ferric ion binding and ferrous ion binding, processes that were not observed in Coho salmon after infestation (Valenzuela‐Muñoz et al . ,). Moreover, RT‐qPCR analysis showed high expression levels of aminolevulinic acid synthase (ALAs) and coproporphyrinogenase , genes involved in the haem biosynthesis process.…”

“…Additionally, iron transport genes such as ferritin, transferrin and IRP were upregulated in Coho salmon skin at early infestation times, while in Atlantic salmon they were overexpressed at 14 dpi (Valenzuela‐Muñoz et al . ,). Also, differences in iron homeostasis genes were observed between Atlantic salmon infested with C. rogercresseyi and L. salmonis .…”

Fishing Into the MicroRNA Transcriptome

“…The miRNA families miR-181, miR-143, and miR-21 were the most abundant in control groups, while miR-21, miR-181, and miR-30 were the most abundant in animals infected with P. salmonis (Valenzuela-Miranda et al, 2017 ). Sea louse Caligus rogercresseyi , which affects Chilean aquaculture, were studied during infestation in Atlantic salmon and the most abundant families were mir-10, mir-21, mir-30, mir-181, and let7 in skin, head and kidney (Valenzuela-Muñoz et al, 2017 ).…”