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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 H, 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. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol 2010; 11:R73. [PMID: 20626842 PMCID: PMC2926784 DOI: 10.1186/gb-2010-11-7-r73] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 05/02/2010] [Accepted: 07/13/2010] [Indexed: 01/08/2023] Open
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.
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Affiliation(s)
- C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Henk Brouwer
- CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | | | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | | | | | - Gregg P Robideau
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Marco Thines
- Biodiversity and Climate Research Centre, Georg-Voigt-Str 14-16, D-60325, Frankfurt, Germany
- Department of Biological Sciences, Insitute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University, Siesmayerstr. 70, D-60323 Frankfurt, Germany
| | - Joe Win
- The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Marcelo M Zerillo
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Gordon W Beakes
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jeffrey L Boore
- Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547, USA
| | - Dana Busam
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Bernard Dumas
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR5546 CNRS-Université de Toulouse, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
| | - Steve Ferriera
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | | | | | - Elodie Gaulin
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR5546 CNRS-Université de Toulouse, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, NL-1-6708 PB, Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB Wageningen, The Netherlands
| | - Laura Grenville-Briggs
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Neil Horner
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jessica Hostetler
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Rays HY Jiang
- The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Justin Johnson
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine-Ramathibodi Hospital, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Haining Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Harold JG Meijer
- Laboratory of Phytopathology, Wageningen University, NL-1-6708 PB, Wageningen, The Netherlands
| | - Barry Moore
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | - Paul Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Vipaporn Phuntmart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Daniela Puiu
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Jyoti Shetty
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Jason E Stajich
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA
| | - Stephan Wawra
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Pieter van West
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Brett R Whitty
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS, Univ. Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS, Univ. Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Frank Martin
- USDA-ARS, 1636 East Alisal St, Salinias, CA, 93905, USA
| | - Paul D Thomas
- Evolutionary Systems Biology, SRI International, Room AE207, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA
| | - Ronald P De Vries
- CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | | | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | - Ned Tisserat
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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