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Annu Rev Phytopathol. 2014;52:19-43. doi: 10.1146/annurev-phyto-102313-045907. Epub 2014 Apr 28.

Harnessing population genomics to understand how bacterial pathogens emerge, adapt to crop hosts, and disseminate.

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Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia 24061; email: ,


Crop diseases emerge without warning. In many cases, diseases cross borders, or even oceans, before plant pathologists have time to identify and characterize the causative agents. Genome sequencing, in combination with intensive sampling of pathogen populations and application of population genetic tools, is now providing the means to unravel how bacterial crop pathogens emerge from environmental reservoirs, how they evolve and adapt to crops, and what international and intercontinental routes they follow during dissemination. Here, we introduce the field of population genomics and review the population genomics research of bacterial plant pathogens over the past 10 years. We highlight the potential of population genomics for investigating plant pathogens, using examples of population genomics studies of human pathogens. We also describe the complementary nature of the fields of population genomics and molecular plant-microbe interactions and propose how to translate new insights into improved disease prevention and control.


disease diagnostics; disease emergence; environmental reservoirs; next-generation sequencing; phylogeography; plant immunity; population genomics

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