Genome evolution in plant pathogenic bacteria

Abstract Bacterial plant pathogens have ravaged crops since the dawn of agriculture and continue to pose a serious threat today. Bacteria and their plant hosts have co-evolved in an evolutionary arms race, with artificial selection due to agriculture tipping the scale in favor of the pathogen. This review gives an overview of plant pathogenic bacterial diversity, showing that pathogenicity has independently evolved numerous times, and that there is not one unifying trait determining plant pathogenicity. Instead, these bacteria represent repeated, independent evolutionary transitions driven by life in complex ecological networks, that include plant hosts, insect vectors, microbial competitors, and highly heterogenous abiotic environments. Their genomes reflect this interplay through a dynamic balance of architecture and flux. These structural features, along with highly variable pangenomes, capture the balance between genome stability and flux imposed by ecological constraints and epidemiological dynamics. Horizontal gene transfer via conjugative plasmids, prophages, integrative and conjugative elements, transposons, and in some lineages, natural competence, remains the major source of adaptive novelty, enabling rapid remodeling of virulence repertoires, metabolic capabilities, and antibiotic or heavy metal resistance genes. These changes create distinct selective landscapes. Agricultural practices such as chemical use, host resistance deployment, or seed trade, can drive recurrent bottlenecks, expansions, and admixture events that leave strong genomic signatures in pathogens. Finally, this review explores the genomic differences enabling the divergence of lifestyles, while also acknowledging knowledge gaps and future directions of research on the evolution of bacterial plant pathogens.