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Background   Pythium ultimum  is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species.    Results  The  P. ultimum  genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related  Phytophthora  species, including the potato blight pathogen  Phytophthora infestans . Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the  P. ultimum  genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to  Phytophthora  species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between  P. ultimum  and more host-specific oomycete species. Although we observed a high degree of orthology with  Phytophthora  genomes, there were novel features of the  P. ultimum  proteome, including an expansion of genes involved in proteolysis and genes unique to  Pythium . We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans.    Conclusions  Access to the  P. ultimum  genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire