Identification and characterization of long non-coding RNAs involved in the formation and development of poplar adventitious roots

Adventitious rooting is essential for vegetative propagation of economically important woody species. A better understanding of the genetic and physiological mechanisms that promote or hinder rooting will enhance the potential for successful commercial deployment of trees. Increasing evidence shows that long non-coding RNAs (lncRNAs) play crucial regulatory roles in a wide range of biological processes. Although a large number of lncRNAs have been identified in plants due to the rapid development of high-throughput sequencing technology in recent years, those in woody plants remain largely unknown. Here, we systematically identified and characterized lncRNAs expressed in different developmental stages of poplar adventitious roots at a genome-wide scale. Through computational analysis, we identified 5952 putative lncRNAs: 4481 intergenic lncRNAs, 761 anti-sense lncRNAs and 710 intronic lncRNAs-for which the structure and expression level differences were analyzed. We also analyzed the different expression levels between protein-coding genes and lncRNAs. The 34 differentially expressed genes were regulated by 144 lncRNAs in cis-action, which provided a new perspective for the regulation of auxin in adventitious root development. In addition, lncRNAs of both lncWOX5 and lncWOX11, which are involved in poplar root development were identified and characterized: lncWOX5 negatively regulated WOX5 and lncWOX11 positively regulated WOX11. Our discovery and characterization of lncWOX5 and lncWOX11 allow for a clearer understanding and preliminarily establishing a theoretical framework for adventitious root formation and development.