Transcriptional regulation of chilling stress responsive long noncoding RNAs in Populus simonii

Abstract

Key messageWe report genome-wide identification and functional prediction of lncRNAs under chilling stress, the present study deepened our understanding of the transcriptional regulation mechanism of poplar under chilling stress.AbstractChilling stress is a major threat to tree development and survival. Long noncoding RNAs (lncRNAs) are known to play a role in plant stress responses, but their transcriptional regulatory network remains elusive. We conducted genome-wide identification and functional prediction of lncRNAs under chilling stress in an ecologically important poplar species, Populus simonii. After the chilling treatment, we detected 30,769 genes and 10,186 putative lncRNAs, of which 13,172 genes and 5082 lncRNAs were differentially expressed under chilling stress in P. simonii. From these chilling-responsive transcripts, we hypothesized that five unique patterns of 21 lncRNAs acted directly on genes, and 617 lncRNAs affected gene expression by interacting with microRNAs (miRNAs). Additionally, the significantly differentially expressed genes were enriched to 198 gene ontology (GO) terms, which were prominently involved in photosynthesis and endogenous phytohormone synthesis pathways. Based on the physiological index, we found 48 genes with 15 lncRNAs, and 70 genes with 50 lncRNAs that were significantly differentially expressed in photosynthesis and endogenous phytohormone synthesis pathways, respectively. These findings improve our understanding of the potential functions of lncRNAs by refining the regulatory roles of lncRNAs in the photosynthesis and phytohormone synthesis pathways.