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

C André Lévesque12, Henk Brouwer3, Liliana Cano4, John P Hamilton5, Carson Holt6, Edgar Huitema4, Sylvain Raffaele4, Gregg P Robideau12, Marco Thines78, Joe Win4, Marcelo M Zerillo9, Gordon W Beakes10, Jeffrey L Boore11, Dana Busam12, Bernard Dumas13, Steve Ferriera12, Susan I Fuerstenberg11, Claire MM Gachon14, Elodie Gaulin13, Francine Govers1516, Laura Grenville-Briggs17, Neil Horner17, Jessica Hostetler12, Rays HY Jiang18, Justin Johnson12, Theerapong Krajaejun19, Haining Lin5, Harold JG Meijer15, Barry Moore6, Paul Morris20, Vipaporn Phuntmart20, Daniela Puiu12, Jyoti Shetty12, Jason E Stajich21, Sucheta Tripathy22, Stephan Wawra17, Pieter van West17, Brett R Whitty5, Pedro M Coutinho23, Bernard Henrissat23, Frank Martin24, Paul D Thomas25, Brett M Tyler22, Ronald P De Vries3, Sophien Kamoun4, Mark Yandell6, Ned Tisserat9 and C Robin Buell5*

  • * Corresponding author: C Robin Buell buell@msu.edu

  • † Equal contributors

Author affiliations

1 Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada

2 Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada

3 CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands

4 The Sainsbury Laboratory, Norwich, NR4 7UH, UK

5 Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA

6 Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA

7 Biodiversity and Climate Research Centre, Georg-Voigt-Str 14-16, D-60325, Frankfurt, Germany

8 Department of Biological Sciences, Insitute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University, Siesmayerstr. 70, D-60323 Frankfurt, Germany

9 Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA

10 School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK

11 Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547, USA

12 J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA

13 Surfaces Cellulaires et Signalisation chez les Végétaux, UMR5546 CNRS-Université de Toulouse, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France

14 Scottish Association for Marine Science, Oban, PA37 1QA, UK

15 Laboratory of Phytopathology, Wageningen University, NL-1-6708 PB, Wageningen, The Netherlands

16 Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB Wageningen, The Netherlands

17 Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK

18 The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA

19 Department of Pathology, Faculty of Medicine-Ramathibodi Hospital, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand

20 Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA

21 Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA

22 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA

23 Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS, Univ. Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France

24 USDA-ARS, 1636 East Alisal St, Salinias, CA, 93905, USA

25 Evolutionary Systems Biology, SRI International, Room AE207, 333 Ravenswood Ave, Menlo Park, CA 94025, USA

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Citation and License

Genome Biology 2010, 11:R73  doi:10.1186/gb-2010-11-7-r73

Published: 13 July 2010

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.