RNA sequencing and functional analyses reveal regulation of novel drought-responsive, long-non-coding RNA in Zanthoxylum bungeanum Maxim

Plant stress tolerance is a complex process involving transcriptional and post-transcriptional regulation of gene expression. Many recent studies have shown that LncRNAs play important roles in plant stress responses and thus create new opportunities for genetic plant breeding. In this study, RNA-seq analysis of Zanthoxylum bungeanum leaves under PEG-simulated drought stress was carried out and differential expression profiles of LncRNAs were obtained. We identified five drought-response-up-regulated LncRNAs (DRURs) and five drought-response-down-regulated LncRNAs (DRDRs). Speculating that these LncRNAs participate in the regulation of Z. bungeanum’s PEG-simulated drought stress response, to confirm their function, we predicted miRNAs in LncRNAs and predicted the miRNA target genes. Forty-four miRNAs were identified from the 10 LncRNAs and the target genes of miRNA were shown to involve numerous signaling pathways and metabolic pathways, including plant-pathogen interaction, plant hormone signal transduction, MAPK signaling, cell growth and death, and amino acid biosynthesis. Results suggest the 10 drought-responsive LncRNAs may be involved in the regulation of membrane stability in mitochondria and chloroplasts and so help maintain normal operation of photosynthesis and respiration. They also, activate the JA, ABA, auxin, ethylene, GA and MAPK signaling pathways.