Transcriptome Profiling Reveals Differential Expression of Virulence Genes in Xylella fastidiosa Cultured Under Different Nutrient Conditions

Xylella fastidiosa is an insect-vectored phytopathogenic bacterium. To capture its adaptation to both nutrient-rich and nutrient-limited environments, we performed transcriptome analyses on two reference strains, Temecula1 and 9a5c, sampled at early- and late-exponential phases in a complex laboratory medium (PWG) and a defined minimum medium (PIM6), representing a nutrient-limited condition inspired by the composition of xylem sap. Across eight conditions (24 transcriptomes), over 90% of annotated coding sequences were expressed, although 40–80% of transcripts exhibited low abundance (TPM < 100). In contrast, a core set of highly abundant transcripts was seen in both strains and media, including the non-coding RNAs 6S and RNase P, as well as multiple colicin- and microcin-like toxins, proteases, lipases, and stress-response factors. Comprehensive pathway reconstruction detected the expression of genes for all essential metabolic pathways, while revealing conditional enrichment of stress-related and defense modules under nutrient limitation. We annotated 5′ and 3′ untranslated regions for thousands of transcripts and defined over 900 operons across both genomes. Differential expression analysis demonstrated that PIM6 medium confers far greater transcriptional reprogramming between early and late phases than PWG. Strain-to-strain comparisons revealed that up to 10.5% of orthologous genes were differentially regulated, emphasizing divergent regulatory networks even under identical growth conditions. This multi-dimensional transcriptome atlas not only refines X. fastidiosa genome annotation but also pinpoints candidate regulators, non-coding RNAs, and operon variants for functional validation. By illustrating the dynamic gene expression landscape of this phytopathogen, our study lays a basis for targeted disruption of key genes and pathways, possibly contributing to novel disease control strategies.