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09 08, 2020;11 (9):

Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon.

Alice Shwe, Tone-Kari Knutsdatter Østbye, Aleksei Krasnov, Sigmund Ramberg, Rune Andreassen
Author Information
  1. Alice Shwe: Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway.
  2. Tone-Kari Knutsdatter Østbye: Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), Postboks 210, NO-1431 Ås, Norway. ORCID
  3. Aleksei Krasnov: Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), Postboks 210, NO-1431 Ås, Norway.
  4. Sigmund Ramberg: Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway.
  5. Rune Andreassen: Department of Life Science and Health, Faculty of Health Sciences, OsloMet‒Oslo Metropolitan University, N-0130 Oslo, Norway. ORCID
PMID: 32911670 DOI: 10.3390/genes11091059

Abstract

Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.

Keywords

Atlantic salmon head kidney miRNA microarray parr-smolt transformation seawater adaptation seawater transfer sequencing smoltification

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MeSH Term

Adaptation, Physiological
Animals
Fish Proteins
Gene Expression Regulation
Gills
Head Kidney
MicroRNAs
RNA, Messenger
Salinity
Salmo salar
Seawater
Sequence Analysis, RNA
Transcriptome

Chemicals

Fish Proteins
MicroRNAs
RNA, Messenger
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

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