Comparative genomics of Phytophthora ramorum

Members of the Phytophthora genus are responsible for many important diseases of plants in agricultural and natural ecosystems. Phytophthora ramorum causes sudden oak death, a disease with devastating effects on oak and tanoak stands in Western US forests. Multiple known lineages express different virulence phenotypes on plant hosts, and characterization of gene content is foundational to understanding the basis for these differences. Recent discovery of P. ramorum at its candidate center of origin in Asia provides a new opportunity for investigating the evolutionary history of the species. The center of origin likely contains basal lineages that would improve accuracy of ancestral state inferences if included in phylogenetic analyses. Our objective was to conduct a pangenomic analysis of newly assembled, high-quality genomes of the sudden oak death pathogen P. ramorum including three isolates from its center of origin in Asia and three lineages causing epidemics in forests. We examined variation of effector content among the sequenced lineages and characterized their evolutionary history in the subclade of Phytophthora containing P. ramorum. We found plasticity among genomes from multiple lineages in a Phytophthora species and provide insights into the evolutionary history of a class of anciently conserved effectors.