A weighted gene co-expression network analysis characterises the common defence responses of Eucalyptus to diverse biotic challenges

Eucalyptus is a globally important forestry genera cultivated for paper, pulp and biofuel production. These trees are increasingly threatened by a range of emerging pests and pathogens. While previous studies have focused on the transcriptomes of single Eucalyptus-pathogen interactions, the core transcriptional networks underlying defence across multiple biotic challenges remain poorly understood. Here we integrated 180 Eucalyptus-biotic stress RNA-sequencing libraries to characterise the common defence gene network during interactions with five distinct pathosystems. We constructed a comprehensive weighted gene co-expression network and identified 38 modules of highly co-expressed genes consisting of between 40 and 3,328 genes. The network revealed distinct modules that were induced by pathogen infection, enriched for defence responses including salicylic acid signalling and secondary metabolite biosynthesis and notably nitrate transport and responses, suggesting a potential link between nitrogen metabolism and immunity. Transcription factor enrichment analysis highlighted WRKY family genes as key regulators of induced responses, with WRKY6 emerging as a candidate hub gene in broad-spectrum resistance. Together, this study provides the first integrative transcriptome network of Eucalyptus responses to diverse biotic stressors, and offers candidate genes and pathways for future functional validation to enhance disease resistance resource in long-lived trees.