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

## TL;DR

This study explores how grapevines respond to Pierce’s disease at different infection stages, identifying key genes involved in defense and stress adaptation.

## Contribution

The study reveals phase-specific transcriptional changes and identifies core regulatory genes during Pierce’s disease progression in grapevines.

## Key findings

- Early infection phase shows strong defense response with 1093 differentially expressed genes.
- Intermediate phase features transcriptional downregulation with 136 differentially expressed genes.
- Key hub genes like chitinase and EDS1 are central to defense and stress adaptation pathways.

## Abstract

Pierce’s disease (PD), caused by the xylem-limited bacterium Xylella fastidiosa, poses a significant threat to global grapevine (Vitis vinifera) 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 V. vinifera responses to X. fastidiosa and provides valuable insights for developing disease-resistant cultivars to mitigate Pierce’s disease.