Research
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
- † Equal contributors
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
Genome Biology 2010, 11:R73 doi:10.1186/gb-2010-11-7-r73
Published: 13 July 2010Abstract
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.
