We redesigned Phytophthora-ID from the ground up in version 2.0 so it is now faster and more stable. We have also developed a new tool for multilocus genotyping of P. ramorum and P. infestans. We hope you enjoy the current implementation.
The sequence based identification module of Phytophthora-ID was created by the Grünwald lab in collaboration with Everett Hansen and Frank Martin, with funding from the Pacific Southwest Research Station, USDA-ARS and the US Forest Service.
The genotype identification module of Phytophthora-ID was created by the Grünwald lab in collaboration with Howard Judelson, Bill Fry, Chris Smart, and Jean Ristaino, with funding from USDA-NIFA and USDA-ARS.
If you use Phytophthora-ID for species identification please cite the following references:
Grünwald, N. J., Martin, F. N., Larsen, M. M., Sullivan, Press, C. M., Coffey, M. D., Hansen, E. M., and Parke, J. L. 2011. Phytophthora-ID.org: A sequence-based Phytophthora identification tool. Plant Disease 95: 337-342.
If you use Phytophthora-ID for multilocus genotype identification of P. ramorum please cite the following references for genotyping protocols, analysis, and interpretation as appropriate:
Goss, E. M., Larsen, M. M., Chastagner, G. A., Givens, D. R., and Grünwald, N. J. 2009. Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries. PLoS Pathogens 5:e1000583.
Grünwald, N. J., E. M. Goss, K. Ivors, M. Garbelotto, F. N. Martin, S. Prospero, E. Hansen, P. J. M. Bonants, R. C. Hamelin, G. Chastagner et al. 2009. Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum. Phytopathology 99: 792-795.
Ivors, K., Garbelotto, M., Vries, I. D., Ruyter-Spira, C., Te Hekkert, B., Rosenzweig, N., and Bonants, P. 2006. Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations. Mol. Ecol. 15:1493-1505.
Prospero, S., Hansen, E. M., Grünwald, N. J., and Winton, L. M. 2007. Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004. Mol. Ecol. 16:2958-2973.
Vercauteren, A., De Debbelaere, I., Grünwald, N. J., Bonants, P., Van Bockstaele, E., Maes, M., and Heungens, K. 2010. Clonal expansion of the Belgian Phytophthora ramorum populations based on new microsatellite markers. Mol. Ecol. 19:92-107.
If you use Phytophthora-ID for multilocus genotype identification of P. infestans please cite the following references for genotyping protocols, analysis, and interpretation as appropriate:
Lees, A.K., R. Wattier, D. S. Shaw, L. Sullivan, N. A. Williams, D. E. L. Cooke. 2006. Novel microsatellite markers for the analysis of Phytophthora infestans populations. Plant Pathology 55:311-319.
Li, Y., D. E. L. Cooke, E. Jacobsen, T. van der Lee. 2013. Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans. Journal of Microbiological Methods 92:316-322. DOI: Doi 10.1016/J.Mimet.2012.11.021.
The Phytophthora-ID (v. 2.0) website was built by Javier Tabima and Nik Grünwald. The BLAST engine was implemented by Javier Tabima. The R functions for visualizing genetic relationships among multilocus genotypes were written by Zhian Kamvar and Javier Tabima as part of the poppr R package and implemented by Javier Tabima and Nik Grünwald. The ITS database is curated by Val Fieland and Nik Grünwald. The cox spacer DB is curated by Frank Martin. The microsatellite datasets were put together by Meg Larsen, Sydney Everhart and Nik Grünwald.
If you have suggestions or questions about Phytophthora-ID please email us at grunwaln(at)science.oregonstate.edu.