Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences

We evaluate the phylogenetic distribution of known, highly virulent plant pathogens in the genus Cochliobolus (sexually reproducing species in the Ascomycota, Pleosporaceae) and assess the relationship between Cochliobolus species and species of Curvularia and Bipolaris (asexual states of fungi in the Ascomycota, Pleosporaceae). To infer a phylogeny, we have used two sequence regions: (i) the complete ITS 1, ITS 2, and 5.8S rDNA sequences for 65 fungal isolates and (ii) a 600 bp fragment of the housekeeping gene gpd, coding for glyceraldehyde-3-phosphate dehydrogenase, for 54 isolates. We combined ITS, 5.8S and gpd sequence data from 41 species. In the Cochliobolus clade, 31 out of 32 species fit clearly into one of two groups. One species, Cochliobolus homomorphus, did not fit clearly into either group. The 13 species in Cochliobolus Group 1 grouped together with 100% bootstrap support from the combined ITS/gpd data. This group included Cochliobolus and Bipolaris species that cause serious crop losses, such as Co. sativus, Co. miyabeanus, Co. carbonum and Co. heterostrophus. However, within Group 1, the known, highly virulent pathogens did not form a monophyletic group of species. Average substitution levels between pairs of species in the Group 1 were low, about 1.7% in the ITS region, suggesting that these species had radiated rapidly and recently. The 18 species in Cochliobolus Group 2 formed a monophyletic group in 96% of parsimony bootstrap replicates of the combined ITS and gpd data. The Cochliobolus species that were transferred into the segregate genus Pseudocochliobolus were in this second group. This study included 9 Curvularia and Bipolaris species without known sexual states and they all appear to be recently derived from among sexual species of Cochliobolus. Both Curvularia and Bipolaris were polyphyletic, but only Bipolaris states were associated with Group 1 Cochliobolus species. Both Curvularia and Bipolaris states were associated with species in Cochliobolus Group 2.