Núñez-Acuña Gustavo, Détrée Camille, Gallardo-Escárate Cristian, Gonçalves Ana Teresa
Interdisciplinary Center for Aquaculture Research (INCAR), Department of Oceanography, University of Concepción, Concepción, Chile.
Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile.
Mar Biotechnol (NY). 2017 Jun;19(3):287-300. doi: 10.1007/s10126-017-9750-z. Epub 2017 May 12.
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.
功能基因组学的出现引发了人们从非模式物种转录组中推断非编码区功能的兴趣。然而，从这个角度来看，许多生物学过程仍未得到充分研究，包括养殖鱼类的肠道免疫。本研究的目的是推断用基于益生菌和益生元的功能性饲料喂养30天的虹鳟（Oncorhynchus mykiss）中长链非编码RNA（lncRNAs）的表达谱。为此，通过Illumina技术进行了全转录组测序，并挖掘lncRNAs以结合已知蛋白质序列评估转录活性。为了检测差异表达的转录本，使用了880个新发现的和9067个先前描述的虹鳟lncRNAs。还分析了lncRNAs的表达水平以及与编码基因的基因组共定位相关性。基因表达的显著差异主要出现在益生菌饲料组，与其他处理相比，该组lncRNAs下调了两倍。不同代谢过程的编码基因在不同饲料之间也存在显著差异。相比之下，lncRNAs与编码基因的基因组共定位在所有饲料组中相似。本研究为鱼类lncRNAs提供了新的知识，表明其在食用具有调节肠道稳态和宿主健康能力的饲料添加剂的鲑鱼中发挥关键作用。
