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.

中文翻译：

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识别和评价长非编码RNA响应处理应力的红Cu鱼（Genypterus chilensis）通过RNA序列。

红鱼（Genypterus chilensis）是一种本地物种，具有强大的潜力来支持智利水产养殖的多样化。在商业条件下，鱼暴露于多种压力下。迄今为止，关于红red的应激反应所涉及的机制知之甚少，并且还没有与长非编码RNA（lncRNA）介导的调控有关的信息。这项工作的目的是首次鉴定G转录组中的lncRNA 。智利并评估在应对压力时肝脏，头部肾脏和骨骼肌中lncRNA的差异表达水平。我们使用以前发布的转录组数据，通过基于几个数据库中的注释信息应用一系列过滤器来丢弃编码序列，从而鉴定出lncRNA。我们在红色鱼的转录组中鉴定出总共14,614个推定的lncRNA，为将来的研究提供了有用的lncRNA参考资源。我们评估了它们在处理肝脏，头部肾脏和骨骼肌中的压力时的差异表达，分别鉴定了112、323和108个差异表达的lncRNA。结果表明，处理红cus鱼的应激反应会改变肝脏的代谢状态，改变头肾的免疫反应，通过重要的编码和非编码基因网络实现骨骼肌萎缩。这是鉴定lncRNAs的第一项研究Genypterus属，它评估硬骨鱼中处理压力和lncRNA之间的关系，从而提供有关Genypterus物种对压力的非编码反应的有价值的信息。