Phytophthora-ID is a tool for the identification of Phytophthora species based on sequence data currently including ITS and cox spacer sequences.
Traditionally identification of species is accomplished by PCR amplification of the Internal Transcribed Spacer (ITS) region followed by either restriction analysis (PhytID) or direct sequencing and a BLAST search against GenBank or other databases. Generally, identification of a species is only as good as the underlying database used. BLAST searches can be problematic as databases accumulate sequences that are mislabeled, of poor quality or otherwise problematic. Phytophthora-ID maintains a database of sequences that is curated to be selective for sequence accessions that come from a trusted source including published, peer-reviewed studies wherever possible. Recently described species that are not yet named in a species paper are only included as Phytophthora taxon “X” to indicate that these might or might not be new species. For more information on a particular species visit PhytophthoraDB that houses much additional information including morphological information on currently described species.
Phytophthora-ID is an ongoing project. Our objective was to create a simple, yet robust site that is easy to use and browse with few bells and whistles. Please provide us with feedback if you find errors or would like to see improvements.
Phytophthora-ID was created by the USDA ARS in collaboration with Oregon State University and the USDA Forest Service, Pacific Southwest Research Station.
NOTE: This resource is still subject to improvements, particularly in the protocols section, but to the best of our knowledge BLAST searches are fully functional and databases are well validated. If you find an error please report it to us.