Identification and dynamic expression profiling of microRNAs and target genes of Paulownia tomentosa in response to Paulownia witches’ broom disease

Paulownia witches’ broom (PaWB) is a disastrous epidemic disease in Paulownia tomentosa trees in many parts of the world. Infected Paulownia tomentosa trees are generally characterized by witches’ brooms, proliferating branches, yellowing and withering leaves, and branch dieback. In previous studies, we found that by treating seedlings with a certain concentration of methyl methanesulphonate (MMS), PaWB could be cured. In this study, three small RNA libraries from healthy, PaWB-infected, and PaWB-infected Paulownia tomentosa treated with MMS were constructed and sequenced by Illumina sequencing and identified approximately 50 conserved and novel microRNAs (miRNAs) in each library. We investigated the expression patterns of the miRNAs in three libraries and found that 20 conserved miRNAs were significantly differently expressed in the comparison (healthy vs. PaWB-infected); nine of these conserved miRNAs were also significantly differently expressed in another comparison (PaWB-infected vs. PaWB-infected MMS-treated). The target genes of these identified miRNAs were found through degradome sequencing platform and functionally annotated. Some of the target genes encoded transcription factors, including auxin response factors, which are known regulators of plant defense responses. Further, we found that the expression levels of some of the miRNA sequences changed in response to MMS treatment and were close to their expression levels in the healthy plantlets. Our results indicate possible roles for Paulownia miRNAs associated with plants infected with PaWB and may provide available information for improving the prevention and treatment of PaWB disease in the future.