Re-evaluation of Japanese Phytophthora isolates based on molecular phylogenetic analyses

•Among 161 isolates, 124 have high homology with their previously identified species.•19 Isolate have high homology with species other than their original identification.•18 Isolates have low homology with any known species, are candidate for new species.•These isolates fall into six groups designated as PNS1–PNS6.•The ITS and coxI genes will be more useful for Phytophthora identification.

Over the past 40 years in Japan, Phytophthora isolates have been collected from various diseased host tissues and infested soils and identified using morphological characters. In order to develop a molecular method for the characterization of Japanese Phytophthora species, we obtained nuclear ribosomal ITS and LSU and mitochondrial coxI DNA sequences from 151 isolates representing 21 known species and 10 unidentified isolates. These were compared with similar sequences from representative isolates of known species. Of these, 124 isolates were found to have been correctly identified. Among the remaining 37 isolates, 19 showed high homology with other described species. The remaining 18 isolates showed only low levels of homology with any known species, and generated monophyletic sub-clades in a phylogenetic tree based on the ITS and nLSU regions and the coxI gene. Therefore, these isolates are candidates for new species, falling into six groups. Together, the Japanese isolates were found to represent phylogenetically diverse groups of species. In a sequence variation analysis, the ITS regions and the coxI genes were found to be more variable than the nLSU sequences, suggesting that they will be more useful for Phytophthora identification.