Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression in response to plant stresses. Given the importance regulatory roles of lncRNAs, providing methods for predicting the function of these molecules, especially in non-model plants, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera (Pistacia vera L.) with 53220 transcripts. In total, we identified 1909 and 2802 salt responsive lncRNAs in Ghazvini, a salt tolerant cultivar, after 6 and 24 h salt treatment, respectively and 1820 lncRNAs in Sarakhs, a salt sensitive cultivar, after 6 h salt treatment. Functional analysis of these lncRNAs by several hybrid methods, revealed that salt responsive NAT-related lncRNAs associated with transcription factors, CERK1, LEA, Laccase genes and several genes involved in the hormone signaling pathways. Moreover, gene ontology (GO) enrichment analysis of salt responsive target genes related to top five selected lncRNAs showed their involvement in the regulation of ATPase, cation transporter, kinase and UDP-glycosyltransferases genes. Quantitative real-time PCR (qRT-PCR) experiment results of lncRNAs, pre-miRNAs and mature miRNAs were in accordance with our RNA-seq analysis. In the present study, a comparative analysis of differentially expressed lncRNAs and microRNA precursors between salt tolerant and sensitive pistachio cultivars provides valuable knowledge on gene expression regulation under salt stress condition.

长的非编码RNA（lncRNA）在响应植物胁迫而调节基因表达中起关键作用。鉴于lncRNA的重要调控作用，研究人员强烈要求提供预测这些分子功能的方法，尤其是在非模型植物中。在这里，我们构建了P. vera（Pistacia vera） lncRNAs的参考序列L.）加上53220笔录。总共，我们在耐盐品种Ghazvini中分别在盐处理6和24小时后鉴定了1909和2802个盐响应lncRNA，在盐处理6 h后在盐敏感品种Sarakhs中鉴定了1820个lncRNA。通过几种杂交方法对这些lncRNA的功能分析表明，盐反应性NAT相关的lncRNA与转录因子，CERK1，LEA，漆酶基因和激素信号通路中涉及的几个基因相关。此外，对与排名前五位的lncRNA相关的盐反应性靶基因的基因本体论（GO）富集分析表明，它们参与了ATPase，阳离子转运蛋白，激酶和UDP-糖基转移酶基因的调控。lncRNA的定量实时PCR（qRT-PCR）实验结果，pre-miRNA和成熟的miRNA与我们的RNA-seq分析一致。在本研究中，对耐盐和敏感开心果品种之间差异表达的lncRNA和microRNA前体的比较分析为盐胁迫条件下的基因表达调控提供了有价值的知识。