Using Differential Expression to Find Treatment and Pathogen Response Genes in Phytophthora ramorum-Tanoak Interactions

Sudden Oak Death (SOD), a disease caused by the pathogen Phytophthora ramorum, has devastated large stands of native oak (Quercus spp.) and tanoaks (Notholithocarpus densiflorus) in California and Oregon. Tanoaks in particular are severely affected by P. ramorum, with the disease threatening to extirpate tanoaks in areas that favor disease.  Phosphonate, a systemic fungicide frequently used to control oomycete pathogens, has shown promise in reducing disease and improving tanoak survival, but its mode of action is not fully understood. Using RNA-seq, we tracked gene expression of host and pathogen in resistant and susceptible trees with or without phosphonate treatment, as well as in trees before and after inoculation. In all we have 46 RNA-seq libraries corresponding to tissue from trees with a range of responses to the pathogen and to phosphonate treatment. Preliminary analysis of differentially expressed genes associated with phosphonate treatment in tanoaks before inoculation with P. ramorum demonstrates up-regulation of genes associated with defense and stress response in trees treated with phosphonate. In full, this work will aid discovery of the genetic underpinning of host-pathogen interactions and identify genes related to the infection process, host resistance, and host response to phosphonate treatment