Paulownia witches’ broom (PaWB) caused by phytoplasma is a destructive disease of Paulownia in China and has been studied over the past 40 years. Recently, our research team found that methyl methanesulfonate (MMS) could help Paulownia plants recover from the symptoms of Paulownia witches’ broom in whichthe expression levels of genes related to photosynthesis, carbohydrate and nitrogen metabolism, plant-pathogeninteraction, circadian rhythm changed. However, the molecular mechanisms underlying the interaction between PaWB and phytoplasma are still not fully understood. Here, high-throughput mRNA sequencing and de novo assembly were conducted in order to investigate gene expression profiles in three Paulownia tomentosa samples (healthy plantlets, diseased plantlets, and diseased plantlets treated with MMS. A total of 85,545 all-unigene were obtained, 2540 of which were significantly differentially expressed among the three samples. Some genes associated with folate and fatty acid synthesis, signal transduction pathways of plant hormones were identified, and their expression patterns were further validated using quantitative real-time PCR. To our knowledge, this is the first transcriptome-based study to demonstrate variations of gene expression related to morphological changes in metabolic pathways of phytoplasma-infected P. tomentosa plants. The information provided in this study will help understand the molecular pathogenesis of the Paulownia plant in response to phytoplasma infection.
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