METAVOLVE: Tracking mechanisms of pathogen emergence with microbiome science and genomics

Pathogens emerge to cause diseases of plants. Next generation sequencing provides an opportunity for surveillance and to describe the specific evolutionary mechanisms that drive emergence. Here I will present our recent work to develop genomic and metagenomic platforms called METAVOLVE to track the genetic basis of active and historical outbreaks from microbiomes and single isolate genome analysis. I will describe specific cases in specialty crops where we described multiyear outbreaks and how we have defined the gene gain and loss that contributed to emergence of pathogens of potato, tomato and geranium.