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Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq

  • Phillip Dettleff
  • Elizabeth Hormazabal
  • Jorge Aedo
  • Marcia Fuentes
  • Claudio Meneses
  • Alfredo Molina
  • Juan Antonio ValdesEmail author
Original Article

Abstract

The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.

Keywords

Long noncoding RNA Genypterus chilensis Red cusk-eel RNA-seq Stress response 

Notes

Acknowledgments

This study was supported by CONICYT/FONDAP/15110027 awarded to Juan Antonio Valdés and Alfredo Molina and CONICYT FONDECYT Postdoctorado 3180283 awarded to Phillip Dettleff.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

10126_2019_9934_MOESM1_ESM.xlsx (38 kb)
ESM 1 (XLSX 38 kb)
10126_2019_9934_MOESM2_ESM.docx (1.1 mb)
ESM 2 (DOCX 1082 kb)

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratory of Molecular Biotechnology, Faculty of Life SciencesAndres Bello UniversitySantiagoChile
  2. 2.Interdisciplinary Center for Aquaculture Research (INCAR)ConcepciónChile
  3. 3.Plant Biotechnology CenterAndres Bello UniversitySantiagoChile
  4. 4.FONDAP Center for Genome RegulationAndres Bello UniversitySantiagoChile
  5. 5.CIMARQAndres Bello UniversityQuintayChile

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