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

Lookup NU author(s): Dr Gordon Beakes



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.

Publication metadata

Author(s): Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CMM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RHY, Johnson J, Krajaejun T, Lin HN, Meijer HJG, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR

Publication type: Article

Publication status: Published

Journal: Genome Biology

Year: 2010

Volume: 11

Issue: 7

Print publication date: 13/07/2010

Date deposited: 29/07/2011

ISSN (print): 1474-7596

ISSN (electronic): 1474-760X

Publisher: BioMed Central Ltd.


DOI: 10.1186/gb-2010-11-7-r73


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Funder referenceFunder name
Dutch Ministry of Agriculture, Nature and Food Quality
Landesstiftung Baden-Wurttemberg
Max-Planck Society
German Science Foundation (DFG)
Hesse's Ministry of Higher Education, Research, and the Arts
2007-35600-18886US Department of Agriculture (USDA) National Institute of Food and Agriculture
2007-35600-17774US Department of Agriculture (USDA) National Institute of Food and Agriculture
2007-35600-18530National Research Initiative of the USDA CSREES
MCB-0731969National Science Foundation
MIEF-CT-2006-022837European Commission
PERG03-GA-2008-230865European Commission
NCRR 1 S10 RR17214-01National Institutes of Health