Phase-Dependent Transcriptional Reprogramming of Vitis vinifera During Pierce’s Disease Progression by Xylella fastidiosa Infection

Pierce's disease (PD), caused by the xylem-limited bacterium <i>Xylella fastidiosa</i>, poses a significant threat to global grapevine (<i>Vitis vinifera</i>) production. Despite its economic importance, the dynamic molecular mechanisms underlying grapevine responses to infection remain poorly understood. This study re-analyzed the publicly available RNA-seq dataset GSE152164 to characterize phase-dependent transcriptional reprogramming during PD progression. Differential expression analysis using DESeq2 identified 1093 differentially expressed genes (DEGs) during the early infection phase (Phase I) and 136 in the intermediate phase (Phase II), indicating a strong early defense response followed by transcriptional downregulation as symptoms progressed. Comparative analysis distinguished 991 Phase-I-specific and 34 Phase-II-specific genes, along with 167 infection-specific temporal DEGs, underscoring a coordinated early immune response and subsequent metabolic repression. Protein-protein interaction network analysis identified 21 high-confidence hub genes, including chitinase (VIT_16s0050g02220), thaumatin-like protein (VIT_02s0025g04250), and EDS1 (VIT_17s0000g07560), which represent core regulators of defense and stress adaptation pathways. Collectively, this study elucidates the transcriptional dynamics underlying <i>V. vinifera</i> responses to <i>X. fastidiosa</i> and provides valuable insights for developing disease-resistant cultivars to mitigate Pierce's disease.