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Pseudomonas syringae genomics: from comparative genomics of individual crop pathogen strains toward population genomics

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Vinatzer, Boris A. | Monteil, Caroline

Edité par CCSD ; Springer-Verlag -

International audience. Whole-genome sequencing (WGS) has become so affordable that we can now sequence genomes of dozens of individuals of a pathogen population instead of sequencing a single representative isolate. This change of framework enables us to answer questions impossible to address just a few years ago. Recent work on the Pseudomonas syringae complex has shown that such genomic approaches have practical implications for disease diagnostics, source attribution, and crop improvement. Most of this work is represented so far by studies on P. syringae pv. aesculi, pv. tomato, pv. actinidiae, and pv. phaseolicola and Pseudomonas cannabina pv. alisalensis. These studies performed comparative genomics and phylogenetic analyses using exclusively populations of P. syringae associated with crops. They thus excluded the vast majority of the P. syringae metapopulation, which is present outside of agricultural fields in habitats associated with the water cycle, leaf litter, and soil, which have been found to be significantly involved in the population dynamics of P. syringae and its evolutionary history. Bulk sequencing of P. syringae strains closely related to pathovar tomato from snowpack and surface water has started to reveal how the genomic diversity of P. syringae in non-agricultural environments relates to that of the epidemic population on crops. This chapter describes how population genomic analyses can take the study of evolution, ecology, disease epidemiology, and molecular plant–microbe interactions of P. syringae to the next level by integrating all of its diversity and how such studies can be applied to help prevent and/or control future disease outbreaks.

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