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Transcriptome Profiling of Long Non-coding RNAs During the Atlantic Salmon Smoltification Process.

Valentina Valenzuela-Muñoz1,2,3, Juan Antonio Váldes4,5, Cristian Gallardo-Escárate4,6

  • 1Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile. valevalenzuela@udec.cl.

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This study reveals long non-coding RNAs (lncRNAs) play a regulatory role in Atlantic salmon parr-smolt transformation. These lncRNAs can serve as novel biomarkers for monitoring fish smoltification and seawater adaptation.

Keywords:
Atlantic salmonRNA-seqSmoltificationTranscriptomelncRNA

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Area of Science:

  • Aquaculture
  • Genomics
  • Molecular Biology

Background:

  • Parr-smolt transformation is critical for salmon aquaculture, involving osmoregulatory changes.
  • Previous research focused on physiological aspects, leaving molecular regulation, particularly lncRNAs, understudied.

Purpose of the Study:

  • To investigate the transcriptional modulation of long non-coding RNAs (lncRNAs) during freshwater to seawater transfer in Atlantic salmon.
  • To identify potential regulatory roles of lncRNAs in the parr-smolt transformation process.

Main Methods:

  • Transcriptome sequencing of gill samples from Atlantic salmon undergoing gradual salinity increase (0 to 30 PSU).
  • Identification and differential expression analysis of long non-coding RNAs (lncRNAs).
  • Correlation expression analysis between lncRNAs and known smoltification-related genes.

Main Results:

  • 2864 putative lncRNAs were identified as differentially expressed during Atlantic salmon smoltification.
  • Most modulated transcripts were downregulated, with the highest number of differentially expressed lncRNAs observed at 30 PSU.
  • Co-localization analysis suggested regulatory roles for specific lncRNAs (e.g., lncRNA_145326, lncRNA_18762) with key genes like Na+/K+-ATPase, growth hormone receptor, and thyroid hormone receptor.

Conclusions:

  • This study provides the first description of lncRNAs with putative regulatory roles in Atlantic salmon during seawater adaptation.
  • Differentially expressed lncRNAs identified can serve as novel biomarkers for monitoring the fish smoltification process.
  • lncRNAs are implicated in regulating crucial biological processes including growth, immune response, and metabolism during parr-smolt transformation.