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The genus  Phytophthora  is agriculturally and ecologically important. As the number of  Phytophthora  species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named  Phytophthora  species. These genetic markers were the cytochrome- c  oxidase 1 ( cox1 ), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β -tub ), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and  tigA  gene fusion protein ( tigA ). As indicated by species distance,  cox1  had the highest genus-wide resolution, followed by ITS,  tigA , and β -tub . Resolution of these four markers also varied with (sub)clade. β -tub  alone could readily identify all species in clade 1,  cox1  for clade 2, and  tigA  for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and β -tub  (96%) were easier to amplify than  cox1  (75%) and  tigA  (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown  Phytophthora  isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.

Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species