Progress 01/15/08 to 10/14/10
Outputs
OUTPUTS: Access to the genome sequence provides a powerful resource to understand mechanisms of pathogenesis by plant pathogens. To assist in further understanding the mechanisms of pathogenicity of Pythium ultimum, a significant plant pathogen, we have completed the sequencing of two strains, DAOM BR144 (also publicly available as ATCC 200006 & CBS 805.95) and DAOM BR748 (= CBS 805.95). We have completed transcriptome analysis of BR144 to identify the expressed portion of the genome and annotated the genome for gene and repetitive sequence content. We have completed analysis of the BR144 genome as well as a comparative analysis with a second strain, BR748. The P. ultimum BR144 genome sequence and annotation is available via a project website (http://pythium.plantbiology.msu.edu/) and through the public repositories at the National Center for Biotechnology Information. We have draft sequenced six additional Pythium species: Pythium ultimum var sporangiiferum, Pythium aphanidermatum, Pythium arrhenomanes, Pythium vexans, Pythium irregulare, and a new Pythium species to further aid in our understanding of genes involved in virulence of this important genus of plant pathogens. We have performed whole transcriptome sequencing for these additional species to annotate the expressed portion of their genomes. PARTICIPANTS: Individuals: Project Director: C. Robin Buell, Associate Investigator, Michigan State University, supervised the project; John Hamilton, Research Assistant, Michigan State University, performed bioinformatic analyses; Ned Tisserat, co-Project Director, Colorado State University Marcelo Zerillo, Postdoctoral Fellow, performed analyses of the Pythium genome and conducted transcriptome studies. Bishwo Adhikari, Postdoctoral Fellow, performed analyses of the Pythium genome. Partner organizations: Andre Levesque, Collaborator, Agriculture and Agri-Food Canada; Sophien Kamoun, Collaborator, Sainsbury Laboratory, United Kingdom; We have also collaborated with a number of scientists throughout the world to annotate and characterize the relevant features of the Pythium genome. Training: Two postdoctoral fellows were trained in genomics and bioinformatics in this project. TARGET AUDIENCES: The target audience is plant pathologists, molecular biologists, genomicists, and bioinformaticists. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
We have generated the first genome sequence for Pythium ultimum, an important plant pathogen. We have established that pyrosequencing using the Roche 454 genome sequencer and the Illumina Genome Analyzer II provides quality sequence information at an efficient cost. We have annotated the P. ultimum BR144 genome and have published a manuscript describing this genome. We have compared the P. ultimum genome with three related oomycete pathogens. Most importantly, we have discovered that this pathogen's genome contains a diverse and unique set of genes involved in pathogenicity and virulence that provides insight into how it causes disease. We have generated a skim sequence of a second strain of P. ultimum for comparative analyses of key components of virulence within this species. We have generated draft genome sequence for six additional species of Pythium. Analysis of these genomes will permit further improvements in our understanding of pathogenicity mechanisms and in development of more robust diagnostic tools for this important genus.
Publications
- Cheung, F., Win, J., Lang, J., Hamilton, J., Vuong, H., Leach, J. E., Kamoun, S., Levesque, C. A., Tisserat, N., and Buell, C.R. 2008. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 9:542.
- Levesque, C.A., Robideau, G.P., de Cock, A.W.A.M., Bala, K., Eggertson, Q., Rintoul, T., Hamilton, J., Tisserat, N., and Buell, C.R. 2010. Genomics and phylogenetics of Pythium species. Contributed poster at the Ninth International Mycological Congress - The Biology of Fungi, Edinburgh, UK, 1-6 August, 2010. Conference Abstracts: P1.146.
- Levesque, C.A., Robideau, G.P., de Cock, A.W.A.M., Bala, K., Eggertson, Q., Rintoul, T., Hamilton, J., Tisserat, N., and Buell, C.R. 2010. The genome of Pythium ultimum provides insight into pathogenicity mechanisms and evolution of oomycetes. Contributed oral presentation at the Joint annual meeting of the Canadian Phytopathological Society and the Pacific Division of the American Phytopathological Society, Vancouver, BC, 20-23 June, 2010. Canadian Journal of Plant Pathology: (Abstract in press).
- Levesque, C. A., Brouwer, H., Cano, L., Hamilton, J. P., Holt, C., Huitema, E., Raffaele, S., Robideau, G. P., Thines, M., Win, J., Zerillo, M. M., Beakes, G. W., Boore, J. L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S. I., Gachon, C. M.M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R.H.Y., Johnson, J., Krajaejun, T., Lin, H., Meijer, H.J.G., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Shetty, J., Stajich, J. E., Trripathy, S., Wawra, S., van West, P., Whitty, B. R., Coutinho, P. M., Henrissat, B., Martin, F., Thimas, P. D., Tyler, B. M., De Vries, R. P., Kamoun, S., Yandell, M., Tisserat, N., and Buell, C. R. 2010. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11:R73.
- Levesque, C.A., Robideau, G.P., de Cock, A.W.A.M., Bala, K., Eggertson, Q., Rintoul, T., Hamilton, J., Tisserat, N., and Buell, C.R. 2010. DNA barcodes, genomics and phylogenetics of Pythium species. Phytopathology 100: S153 (Abstract). Invited oral presentation at the Annual meeting of the American Phytopathological Society. Special Session entitled "Cryptic Foes: Gathering the Latest Advances on Pythium". Charlotte, NC, USA, 7-11 August, 2010.
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