Raw data underlying the publication: Multi-Omics Insights into Genomic and Metabolomic Plasticity Driving Pathogenic-Beneficial Divergence and Virulence Mechanisms in Pantoea ananatis

The dataset encompasses genomic, metabolomic, and phenotypic data from 18 <em>Pantoea ananatis</em> isolates derived from mulberry (<em>Morus</em> spp.), focusing on eco-evolutionary mechanisms underlying their pathogen-probiotic duality. Key findings include three genetic clades: low-virulence probiotics (Pa-I, 11 strains), high-virulence pathogens (Pa-II, 5 strains), and transitional (Pa-III, 2 strains). Representative strains Pa-6 (probiotic) and YSFJ (pathogen) highlight divergences in genome architecture (e.g., plasmids, pseudogenes), metabolomes (e.g., TCA/amino acid vs. phosphonate/sulfur pathways), pan-genome openness, multidrug resistance, and host interactions (e.g., mild colonization enhancing resilience vs. aggressive lysis accelerating dysbiosis). This supports predictive frameworks for biocontrol and resilient microbiome engineering in agriculture. Data types include raw sequencing reads, MS spectra, bioassay results, and figure sources, organized by category. Total size: approximately 10-15 GB. Ethical compliance: Biosafety protocols followed; no human/animal subjects. Contact corresponding authors for interpretation queries on genomic evolution or metabolomic networks.