A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

Plants and pathogens evolve in response to each other. This coevolutionary arms race is fueled by genetic variation underlying the recognition of pathogen proteins by the host and the defeat of host defenses by the pathogen. Together with new mutations, genetic diversity in populations of both the host and pathogen represent a pool of possible variants to maintain adaptation via natural selection. Drastic changes in genetic diversity in crop species have occurred as a consequence of domestication. Whether changes in the genetic composition of these host populations also have affected genetic diversity in pathogen species is, so far, poorly understood. Advances in comparative genomics and population genomic approaches open new avenues to study adaptive processes in plant pathogens and to infer the impact of agro-ecosystems on the evolution of pathogen populations. Here we summarize new insights gained from comparative genome studies and population genomics in host-pathogen systems.