Comparative and functional genomics in downy mildew pathogens

The downy mildews are highly specialized plant pathogens that cause disease on many agriculturally important plants worldwide. Genome sequencing of diverse species and populations has provided new opportunities to understand the mechanism and evolution of pathogenicity in the downy mildews and other oomycetes. We have sequenced the genomes of Bremia lactucae (lettuce downy mildew) and Peronospora tabacina (tobacco downy mildew) as well as several other related species. Genes encoding effector proteins are important in plant pathology because they are both determinants of host resistance and contributors to virulence through manipulation of host physiology and immune suppression. We used several complementary bioinformatic approaches to discover candidate genes encoding effectors in downy mildew genomes on the basis of conserved protein structural motifs, lineage specificity, and species-level diversity. While effector candidates from Phytophthora have been typically predicted using the N-terminal RXLR motif, we found that we were able to predict additional candidates for downy mildews by searching for WY motifs in the C-teminal domain.  Many of these WY effector candidates have RXLR-like motifs that were not detected using the Phytophthora-trained HMM model. These candidate effectors are being functionally tested in planta for suppression of cell death activity. Effector identification provides the foundation for research into the molecular mechanisms of downy mildew pathogenesis and will be valuable for germplasm screening and field pathogenomics.