Divergent and Convergent Modes of Host-Pathogen Interaction Revealed By the Comparative Gene Co-Expression Network and Genome Analyses of Puccinia graminis f. sp. tritici Isolates on a Susceptible Wheat Host

The arms race between plants and pathogens exerts evolutionary pressure on pathogens to diversify in order to evade host-plant defenses. To better understand how the diversified arsenal of fungal genes helps to establish interaction with a compatible wheat line, we performed a comparative genomic analysis of two American isolates of Puccinia graminis f. sp. tritici (Pgt). Inter-isolate divergence in the secreted effector encoding genes was compared with the level of divergence of host-pathogen gene co-expression networks (GCN). This comparison revealed substantial differences in the secreted protein encoding genes of each Pgt isolate, which are reflected by altered host-plant gene expression patterns during infection. The Gene Ontology analyses of GCNs developed for different isolates identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and correlated positively with the proportion of conserved effectors in a given sub-network. While the diverged Pgt isolates tended to exploit similar host biological pathways for infection, the mode of interaction varied for different pathways. Some pathways were associated with the conserved set of secreted protein encoding gene and others were linked with the diverged or isolate-specific effector encoding genes. The latter indicates that different fungal isolates likely can utilize different sets of secreted proteins to target the same biological pathways. These results suggest that the diversification of effector encoding genes provides diverse and flexible mechanisms for establishing compatible host-pathogen interaction.