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

C. Andre Levesque, Henk Brouwer, Liliana Cano, John P. Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P. Robideau, Marco Thines, Joe Win, Marcelo M. Zerillo, Gordon W. Beakes, Jeffrey L. Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I. Fuerstenberg, Claire M. M. Gachon, Elodie Gaulin, Francine GoversLaura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays H. Y. Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold J. G. Meijer, Barry Moore, Paul Morris, Vipaporn Phuntmart, Daniela Puiu, Jyoti Shetty, Jason E. Stajich, Sucheta Tripathy, Stephan Wawra, Pieter van West, Brett R. Whitty, Pedro M. Coutinho, Bernard Henrissat, Frank Martin, Paul D. Thomas, Brett M. Tyler, Ronald P. De Vries, Sophien Kamoun, Mark Yandell, Ned Tisserat, C. Robin Buell

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    Abstract

    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.

    Original languageEnglish
    Article numberR73
    Pages (from-to)-
    Number of pages22
    JournalGenome Biology
    Volume11
    Issue number7
    DOIs
    Publication statusPublished - 2010

    Keywords

    • OOMYCETE PHYTOPHTHORA-INFESTANS
    • POTATO FAMINE PATHOGEN
    • PROTEIN FAMILIES
    • MITOCHONDRIAL GENOME
    • PLEIOTROPIC DRUG
    • GENE FAMILY
    • ARABIDOPSIS-THALIANA
    • CADHERIN SUPERFAMILY
    • MICROBE INTERACTIONS
    • MOLECULAR EVOLUTION

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