# A systems biology framework integrating cross-species transcriptomics and PPI networks for Xylella fastidiosa resistance gene identification

## TL;DR

This study identifies 18 conserved genes involved in plant resistance to Xylella fastidiosa, a harmful bacterium, by analyzing gene activity across four plant species.

## Contribution

A novel core resistance network of 18 conserved genes against Xylella fastidiosa was identified through cross-species transcriptomics and PPI networks.

## Key findings

- 18 conserved genes and 1852 divergent expression patterns were identified across four plant species.
- The genes are involved in structural reinforcement, stress signaling, antimicrobial compound production, and resource optimization.
- Protein-protein interaction networks revealed immune hubs like BAK1, WRKY33, and WRKY40 with new connections to proteases and ubiquitin components.

## Abstract

Xylella fastidiosa, a highly pathogenic, xylem-limited, gram-negative bacterial species, represents a significant threat to many plant species, including olive, almond, grapevine, and alfalfa. Through cross-species transcriptomic analysis of Olea europaea, Prunus dulcis, Vitis vinifera, and Medicago sativa, we identified a novel core resistance network consisting of 18 conserved genes against Xylella fastidiosa, alongside 1852 divergent expression patterns. These common genes may play a crucial role in orchestrating a multi-layered plant defense response, enabling (1) structural reinforcement as well as facilitating cuticular wax biosynthesis (KCS11 and KAS1); (2) stress signaling mediated by hormonal crosstalk involving jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) mediated by the genes AOS and CYP707A4, alongside calcium signaling through ACA12 gene; (3) antimicrobial 22 compound production (β-amyrin synthase BAS, ABC transporter PDR6); and (4) resource optimization through trehalose metabolism (AT1G23870) and amino acid transport (AAP2). The protein-protein interaction networks revealed coordinated regulation of immune hubs including BAK1, WRKY33, and WRKY40, with novel connections to subtilase proteases and ubiquitin-proteasome components. This conserved molecular framework highlights evolutionary convergence in plant defenses against xylem pathogens, providing future targets for engineering resistance through cell wall modification, stress signaling potentiation, and secondary metabolite engineering.

The online version contains supplementary material available at 10.1186/s12870-025-07102-8.