LncRNA/circRNA–miRNA–mRNA networks regulate the development of root and shoot meristems of Populus

Root and shoot meristems play essential roles in the formation and development of plant tissues and organs. However, little is known about the roles of non-coding RNAs (ncRNAs) in the regulation of maintenance and differentiation of root and shoot meristems in Populus. Here, we first identified and characterized many microRNAs (miRNAs), mRNAs, long ncRNAs (lncRNAs) and circular RNAs (circRNAs) from the root tip and shoot tip of poplar at the genome-wide level. A total of 73,012 mRNAs, 13,099 lncRNAs, 47 circRNAs, and 114 miRNAs were identified by strand-specific RNA sequencing and small RNA sequencing. Differential expression analysis revealed that there were 8501 differentially expressed (DE) mRNAs, 295 DE lncRNAs, 15 DE circRNAs and 45 DE miRNAs, and their functions were annotated. Some lncRNAs and circRNAs have miRNA binding sites, and these ncRNAs may act as functional endogenous pseudo target mimics. Therefore, we constructed lncRNA − peu-miR394a-5p − mRNA, lncRNA − peu-miR166a − mRNA, lncRNA/circRNA − peu-miR396a − mRNA and lncRNA/circRNA − peu-miR160a − PeARF regulatory networks and verified the target genes of these four miRNAs by degradome sequencing. Furthermore, by overexpressing pei-miR160a, we found that pei-miR160a negatively regulated the expression of six PeARFs, five lncRNAs and one circRNA. Our findings provide new insights into the lncRNA/circRNA − miRNA − mRNA networks involved in the development of the root and shoot meristems of Populus.