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United States Department of Agriculture

Agricultural Research Service

Title: Phytophthora-ID.org: a sequence-based Phytophthora identification tool

Authors
item Grunwald, Niklaus
item Martin, Frank
item Larsen, Meredith
item Sullivan, Christopher -
item Press, Caroline
item Coffey, Michael -
item Hansen Everett, M -
item Parke, Jennifer -

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 25, 2010
Publication Date: March 15, 2011
Citation: Grunwald, N.J., Martin, F.N., Larsen, M.M., Sullivan, C.M., Press, C.M., Coffey, M.D., Hansen Everett, M., Parke, J.L. 2011. Phytophthora-ID.org: a sequence-based Phytophthora identification tool. Plant Disease. 95(3):337-342.

Interpretive Summary: Identification of biological species in our day and age relies on DNA sequencing and searching of a sequence against databases. Phytophthora species are an important group of plant pathogens affecting many crops. We developed the Phytophthora ID website, which contains two web-based, searchable databases for rapid identification of Phytophthora species based on DNA sequences for two distinct, genetic regions. The databases were validated with 700 Phytophthora isolates collected from nursery environments during 2006 to 2009. These novel databases and Phytophthora identification tools can be found at www.Phytophthora-ID.org.

Technical Abstract: Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed the Phytophthora ID website, which contains two web-based, searchable databases for rapid identification of Phytophthora species based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase (cox) 1 and 2 spacer region followed by BLAST searching the database. Both databases are highly selective and for ITS include only sequences that are associated with published Phytophthora species descriptions or classic Phytophthora phylogenetics references. For the cox spacer region, data was obtained by resequencing select isolates associated with published work. Novel taxa tentatively named are selectively included and labeled as Phytophthora taxon "X" as in, for example, P. taxon “asparagi”. The databases were validated with 700 Phytophthora isolates collected from nursery environments during 2006 to 2009. This resource, found at www.Phytophthora-ID.org, is a robust and validated tool for identification of Phytophthora species and is actively being maintained.

Last Modified: 4/18/2014
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