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Marine Biotechnology

, Volume 19, Issue 3, pp 287–300 | Cite as

Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss

  • Gustavo Núñez-Acuña
  • Camille Détrée
  • Cristian Gallardo-Escárate
  • Ana Teresa GonçalvesEmail author
Original Article

Abstract

The advent of functional genomics has sparked the interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, numerous biological processes remain understudied from this perspective, including intestinal immunity in farmed fish. The aim of this study was to infer long non-coding RNA (lncRNAs) expression profiles in rainbow trout (Oncorhynchus mykiss) fed for 30 days with functional diets based on pre- and probiotics. For this, whole transcriptome sequencing was conducted through Illumina technology, and lncRNAs were mined to evaluate transcriptional activity in conjunction with known protein sequences. To detect differentially expressed transcripts, 880 novels and 9067 previously described O. mykiss lncRNAs were used. Expression levels and genome co-localization correlations with coding genes were also analyzed. Significant differences in gene expression were primarily found in the probiotic diet, which had a twofold downregulation of lncRNAs compared to other treatments. Notable differences by diet were also evidenced between the coding genes of distinct metabolic processes. In contrast, genome co-localization of lncRNAs with coding genes was similar for all diets. This study contributes novel knowledge regarding lncRNAs in fish, suggesting key roles in salmons fed with in-feed additives with the capacity to modulate the intestinal homeostasis and host health.

Keywords

Long non-coding RNA Oncorhynchus mykiss RNA-seq Functional diets 

Notes

Acknowledgements

This study was financially supported by CONICYT-Chile through the grants FONDECYT Postdoctoral 3140183 and FONDAP-INCAR 15110027. The authors thank EWOS-Cargill for supplying the feed and oil mixture for the trial and for granting access to experimental feeding unit in Coronel Chile. The authors would also like to thank Fernando Vidal and Alejandro Capdeville for the technical support during experimental feed preparation.

Compliance with Ethical Standards

Ethical Statement

All animals used in this study were treated in accordance to the Biosecurity Regulations and Ethical Protocols approved by Universidad de Concepción Ethics Committee as a mandatory part of the Postdoctoral FONDECYT Grant 3140183 granted by the CONICYT-Chile.

Conflict of Interest

The authors declare that they have no conflicts of interest.

Supplementary material

10126_2017_9750_MOESM1_ESM.docx (46 kb)
Table S1 (DOCX 46 kb)
10126_2017_9750_MOESM2_ESM.docx (122 kb)
Table S2 (DOCX 121 kb)
10126_2017_9750_MOESM3_ESM.docx (140 kb)
Table S3 (DOCX 140 kb)

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Gustavo Núñez-Acuña
    • 1
  • Camille Détrée
    • 1
  • Cristian Gallardo-Escárate
    • 1
  • Ana Teresa Gonçalves
    • 1
    • 2
    Email author
  1. 1.Interdisciplinary Center for Aquaculture Research (INCAR), Department of OceanographyUniversity of ConcepciónConcepciónChile
  2. 2.Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR)University of ConcepciónConcepciónChile

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