The most accurate method for identification of isolates to a species level is DNA sequence analysis. A range of loci have been used for this purpose, with perhaps the most extensive database available for the nuclear encoded ITS region of the rDNA. Additional nuclear loci include β-tubulin, translation elongation factor 1α, elicitin, 60S Ribosomal protein L10, enolase, heat shock protein 90, TigA gene fusion protein, and the large subunit of the rDNA (Blair et al. 2008; primers for amplification for these loci and sequence data for all species in the genus may be downloaded at link to the genetic marker page). Additional nuclear loci, such as the ras-related protein Ypt1, is also available for some species (Schena et al. 2007). Mitochondrial genes such as cox2 and cox1 (Martin and Tooley 2003a, b), cox1 and nad1 (Kroon et al. 2004) have also been used (primers for amplification of cox2 and sequence data for all species in the genus may be downloaded at link to the genetic marker page). In addition, the same isolates that were examined in the multigene phylogeny of Blair et al. (2008) have had the nad9, rps10, and secY genes sequenced, this data will be available on the database shortly. With the current effort to include the genus in the Tree of Life initiative a more extensive sequence data set for a portion of the cox1 gene is currently being collected (A. Levesque and M. Coffey, unpublished).
Schena and Cooke (2006) have identified 4 intergenic regions from the mitochondrial DNA, a portion of the intergenic region of the rDNA, and spacer regions of the ras-related protein Ypt1 that can be useful for identification of species and subpopulations within a species (overview)
Kroon LP, Bakker FT, van den Bosch GB, Bonants PJ, Flier WG. 2004 Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genetics and Biology 41:766-782
Martin, F.N and Tooley, P.W. (2003) Phylogenetic relationships of Phytophthora ramorum, P. nemorosa, and P. pseudosyringae, three species recovered from areas in California with sudden oak death. Mycological Research 107:1379-1391. (pdf of reprint)
Frank N. Martin,Paul W. Tooley 2003 Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes Mycologia 95:269-284 (pdf of reprint)
Schena, L., Duncan, J.M., Cooke, D.E.L. 2008 Development and application of a PCR-based 'molecular tool box' for the identification of Phytophthora species damaging forests and natural ecosystems. Plant Pathology 57:64-75