Introduction: Phytoplasma disease significantly affects stone fruit trees worldwide, leading to symptoms such as witches' broom, decline, and eventual plant death. To explore its impact on peaches, we analyzed the transcriptomic profiles of diseased and healthy cherry plants. Several genes with differential expression were identified, most of which were involved in amino acid metabolism and secondary metabolite biosynthesis pathways, showing altered expression in phytoplasma-infected trees.Materials and Methods: Total RNA was extracted from both infected and healthy peach leaves, and cDNA synthesis was performed for qRTPCR analysis. Transcriptome sequencing data from infected cherry plants were collected and analyzed. Using Cytoscape, ten hub genes in the protein-protein interaction (PPI) network were identified, with five genes showing higher degrees of interaction. These hub genes were validated in peach plants using quantitative PCR (qRT-PCR).Results: The study revealed increased expression of DNA-directed ۵'-۳' RNA polymerase activity in differentially expressed genes (DEGs) and hub genes, which were associated with disease occurrence, but no significant expression changes were observed in other selected genes in infected leaves. This study showed that the high expression of RNA polymerase genes in phytoplasma-infected cherry and peach plants depends on amino acid biosynthesis and secondary metabolite pathways.Conclusions: This research provides a deeper understanding of the genetics and molecular processes in plants, which could enable researchers to improve traits in stone fruit trees in response to phytoplasma disease using advanced genome editing techniques. These findings could lead to the development of new, more resistant, and higher-yielding cultivars. The gene identified in this study serves as a promising biomarker for early detection of phytoplasma infection in stone fruits and offers insights for disease control strategies.
