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The causal agent of flag smut of wheat is currently subject to strict quarantine regulations in many countries and is believed to have a wide host range on wild and cultivated grasses. This fungus has been classified as both Urocystis agropyri and Urocystis tritici. Urocystis agropyri was first described from Elymus repens in Germany and U. tritici was first described from Triticum vulgare (=T. aestivum). In 1953, G. W. Fischer placed U. tritici and a large number of other Urocystis species in synonymy with U. agropyri. The present study is the first attempt to clarify the taxonomy and phylogeny of flag smut pathogens of grasses using molecular analyses. Three loci, the internal transcribed spacer (ITS) region of rDNA, the RNA polymerase II subunit 2 (RPB2), and translation elongation factor (TEF) protein-coding regions were used for phylogenetic reconstruction to determine the species boundaries of 24 Urocystis specimens from triticoid hosts. Results indicate that there are several distinct lineages of flag smut pathogens, including the causal agent of flag smut of wheat, which is supported as a separate species, U. tritici. Sequences from specimens on E. repens, which are retained as U. agropyri, grouped in a clade distinct from those on wheat and rye. The closest relatives of U. tritici were found to be U. hispanica from Aegilops and Urocystis sp. from Thinopyrum junceiforme and Elymus trachycaulis. Recognition that U. tritici is genetically distinct from U. agropyri sensu stricto will impact regulatory policy and facilitate the development of diagnostic tests.
