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

Marine Biotechnology
Gustavo Núñez-AcuñaAna Teresa Gonçalves

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 ...Continue Reading

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Citations

Sep 20, 2018·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Rochelle C JoslynRam Savan
Dec 14, 2018·Frontiers in Immunology·Man WangKun Wang
Nov 9, 2018·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Ana Teresa GonçalvesCristian Gallardo-Escárate
Feb 28, 2021·Marine Biotechnology·Valentina Valenzuela-MuñozCristian Gallardo-Escárate
Jul 11, 2021·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Guoqiang LuZiping Zhang

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Methods Mentioned

BETA
reverse transcription-PCR
RNA-seq

Software Mentioned

BlastN
JMP
CLC
BlastX
CPAT Coding Potential Assessment Tool
Corrplot
Large Gap Read Mapping
Blast2GO
CLC Genomics Workbench
CLC Genomic Workbench

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