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A comprehensive exploration of common and specific plant responses to biotrophs and necrotrophs is necessary for a better understanding of plant immunity. Here, we compared the  Arabidopsis  defense responses evoked by the biotrophic fungus  Golovinomyces orontii  and the necrotrophic fungus  Botrytis cinerea  through integrative network analysis. Two time-course transcriptional datasets were integrated with an  Arabidopsis  protein-protein interaction (PPI) network to construct a  G. orontii  conditional PPI sub-network (gCPIN) and a  B. cinerea  conditional PPI sub-network (bCPIN). We found that hubs in gCPIN and bCPIN played important roles in disease resistance. Hubs in bCPIN evolved faster than hubs in gCPIN, indicating the different selection pressures imposed on plants by different pathogens. By analyzing the common network from gCPIN and bCPIN, we identified two network components in which the genes were heavily involved in defense and development, respectively. The co-expression relationships between interacting proteins connecting the two components were different under  G. orontii  and  B. cinerea  infection conditions. Closer inspection revealed that auxin-related genes were overrepresented in the interactions connecting these two components, suggesting a critical role of auxin signaling in regulating the different co-expression relationships. Our work may provide new insights into plant defense responses against pathogens with different lifestyles.

Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections