Integration of small RNAs, degradome, and transcriptome sequencing in Populus × euramericana “Neva” provides insights into the allelopathic interference of para-hydroxybenzoic acid

Allelopathy is a hot topic of research; however, little is known regarding microRNA (miRNA) expression profiles in plants in response to allelochemicals. In this study, we combined the analyses of the transcriptome, small RNAs (sRNAs), and the degradome to identify key regulatory miRNA-targeted circuits under para-hydroxybenzoic acid (pHBA) stress. A total of 739 and 673 miRNAs were identified in leaves and roots, respectively. Of those, 214 and 148 miRNAs were significantly differentially expressed and identified as pHBA-responsive miRNAs in leaves and roots, respectively. The target genes for the pHBA-responsive miRNAs are involved in signal transduction, response to stress, and secondary metabolite pathways. Furthermore, an integrated analysis of the miRNA–target expression profiles was used to screen the 60 differentially expressed target genes from the 46 differentially expressed miRNAs in the leaves and the 51 differentially expressed target genes from the 36 differentially expressed miRNAs in roots. This integrated analysis revealed 17 and 30 pairs of miRNA targets in the leaves and roots, respectively, which had negatively correlated expression profiles. According to a real-time quantitative polymerase chain reaction (PCR) analysis, 14 miRNA–target pairs also exhibited negative correlations. Moreover, four coexpression regulatory networks were constructed based on the profiles of the differentially expressed miRNA–target pairs. These results suggest that comprehensive analyses of transcriptomes, sRNAs, and the degradome provide a useful platform for investigating the molecular mechanism underlying the pHBA-induced stress response in plants.