Pseudomonas syringae coffee blight is associated with the horizontal transfer of plasmid-encoded type III effectors.

The emergence of new pathogens is an ongoing threat to human health and agriculture. While zoonotic spillovers received considerable attention, the emergence of crop diseases is less well studied. Here, we identify genomic factors associated with the emergence of Pseudomonas syringae bacterial blight of coffee. Fifty-three P. syringae strains from diseased Brazilian coffee plants were sequenced. Comparative and evolutionary analyses were used to identify loci associated with coffee blight. Growth and symptomology assays were performed to validate the findings. Coffee isolates clustered in three lineages, including primary phylogroups PG3 and PG4, and secondary phylogroup PG11. Genome-wide association study of the primary PG strains identified 37 loci, including five effectors, most of which were encoded on a plasmid unique to the PG3 and PG4 coffee strains. Evolutionary analyses support the emergence of coffee blight in PG4 when the coffee-associated plasmid and associated effectors derived from a divergent plasmid carried by strains associated with other hosts. This plasmid was only recently transferred into PG3. Natural diversity and CRISPR-Cas9 plasmid curing were used to show that strains with the coffee-associated plasmid grow to higher densities and cause more severe disease symptoms in coffee. This work identifies possible evolutionary mechanisms underlying the emergence of a new lineage of coffee pathogens.

Towards integrative plant pathology.

The field of plant pathology has revealed many of the mechanisms underlying the arms race, providing crucial knowledge and genetic resources for improving plant health. Although the host-microbe interaction seemingly favors rapidly evolving pathogens, it has also generated a vast evolutionary history of largely unexplored plant immunodiversity. We review studies that characterize the scope and distribution of genetic and ecological diversity in model and non-model systems with specific reference to pathogen effector diversity, plant immunodiversity in both cultivated species and their wild relatives, and diversity in the plant-associated microbiota. We show how the study of evolutionary and ecological processes can reveal patterns of genetic convergence, conservation, and diversification, and that this diversity is increasingly tractable in both experimental and translational systems. Perhaps most importantly, these patterns of diversity provide largely untapped resources that can be deployed for the rational engineering of durable resistance for sustainable agriculture.