Phylogenetic relationships of sugarcane rust fungi

The phylogenetic positions of Puccinia spp. infecting sugarcane (a complex hybrid of Saccharum spp.) were determined using 38 newly generated rust sequences and 26 sequences from GenBank. Rust specimens on sugarcane were collected from 164 locations in 23 countries and identified based on light microscopy. The morphology for all samples matched that of Puccinia kuehnii or P. melanocephala, the orange and brown rust pathogens of sugarcane, respectively. Nuclear ribosomal DNA sequences (rDNA) including portions of the 5.8S rDNA, the complete internal transcribed spacer 2 (ITS2) and 5' region of the large subunit (nLSU) rDNA were obtained for each species along with 36 additional rust taxa. Despite a shared host, the two Puccinia spp. on sugarcane are not closely related within the Pucciniales. Phylogenetic analyses place P. melanocephala most closely to P. miscanthi, P. nakanishikii, and P. rufipes infecting Miscanthus sinensis, Cymbopogon citratus, and Imperata cylindrica, respectively. Puccinia kuehnii is basal to a clade of Poaceae-infecting rusts including P. agrophila, P. polysora, P. substriata, and Uromyces setariae-italicae infecting Schizachyrium spp., Zea mays, Digitaria spp., and Urochloa mosambicensis, respectively. Light and scanning electron microscopy images highlight morphological differences distinguishing the two sugarcane-infecting species. This study confirms the separation of rust species infecting Poaceae from Cyperaceae- and Juncaceae-infecting rusts and also provides support for the presence of an additional group that includes P. kuehnii and other grass-infecting relatives.