Exploration of Key Functional Genes Affecting Witches’ Broom Disease in Paulownia fortune i Based on RNA‐Seq

Paulownia witches’ broom ( Pa WB) disease caused by a phytoplasma infection has limited the development of the Paulownia industry. The molecular mechanism underlying Pa WB disease remains poorly characterized. In this study, the following samples served as the experimental materials: uninfected Paulownia fortunei seedlings, phytoplasma‐infected P. fortunei seedlings, phytoplasma‐infected P. fortunei seedlings treated with 20 mg L ⁻¹ methyl methanesulfonate (MMS), and phytoplasma‐infected P. fortunei seedlings that underwent a simulated recovery. High‐throughput transcriptome sequencing technology (RNA‐seq) was used to analyze the gene expression profiles of the P. fortunei samples during the phytoplasma infection and the subsequent recovery process. We identified 1,549,905,681 clean reads and found that TSS and TTS as the predominant AS events. AP2/ERF‐ERF, MYB, NAC, C2H2, and TCP were enriched TFs in the 10 analyzed samples. Additionally, a weighted gene co‐expression network analysis revealed two modules related to Pa WB disease. Finally, we identified nine genes associated with photosynthesis (e.g., protein plastid movement impaired 2, PMI2; weak chloroplast movement under blue light 1, WEB1), plant hormones (e.g., 9‐cis‐epoxycarotenoid deoxygenase, NCED), and the cell wall (e.g., polygalacturonase, PG) that may be related to the pathogenesis of Pa WB disease. The data generated in this study may be useful for identifying genes encoding proteins with inhibitory effects on phytoplasma growth and reproduction. These genes may be relevant for increasing the disease resistance of Paulownia species.