Abstract
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.
Highlights
Pistacia belongs to Anacardiaceae family and contains 13 or more species, which among them pistachio (Pistacia vera L.) is the only cultivated and economically important species that is called as the ‘green gold tree’
Researches on pistachio are often focused on genetic diversity, genetic relationships and sex determination by using of different molecular markers such as simple sequence repeat (SSR)[19,20,21], amplified fragment length polymorphism (AFLP)[22,23], inter-simple sequence repeats (ISSR)[5,24,25,26,27], randomly amplified polymorphic DNA (RAPD)[28,29,30], retrotransposon microsatellite amplified polymorphism (REMAP)[31], selective amplification of microsatellite polymorphic loci (SAMPL)[32] and single nucleotide polymorphism (SNP)[33]
RNA sequencing of pooled sample including three tissues and two salt tolerant and sensitive pistachio cultivars under control and four time points after salt treatment was done by Illumina Hiseq 2000 platform for building a reference transcriptome[35]
Summary
Pistacia belongs to Anacardiaceae family and contains 13 or more species, which among them pistachio (Pistacia vera L.) is the only cultivated and economically important species that is called as the ‘green gold tree’. Further studies indicated that they extensively distribute in different part of the genomes including introns, intergenic regions, antisense transcripts, pseudogenes and retrotransposons[42] They involve in gene expression regulation in different ways such as interaction with DNA, mRNA, miRNA and protein that lead to regulation of gene expression at the transcriptional, post-transcriptional, epigenetic, translational, and post-translational levels. QRT-PCR results confirmed that all selected salt responsive lncRNAs respond to salt stress These results suggested that at least a subset of these newly identified differentially expressed lncRNAs may play important roles in response to salinity stress in this plant. New generation of lncRNA-SSR markers can be used for different marker based studies in this economically important species
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
