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Oomycetes, such as Phytophthora spp., establish pathogenic interactions with a diversity of plants, but the molecular mechanisms underlying these diseases remain poorly characterized. However, research on Phytophthora pathosystems has accelerated significantly with ongoing advances in microbial and plant genomics and the resulting resources. A variety of functional analyses are being used to associate gene sequences with key processes that regulate interactions between these important pathogens and their hosts. Data from such analyses are starting to shed light on the relationship between pathogen molecules that manipulate host cell structure and function and the innate defense response in plants.