The nucleotide sequences of the 5' end of the nuclear large subunit ribosomal RNA were obtained for 15 basidiomycetes representing a diversity of orders, including Agaricostilbales, Atractiellales, Auriculariales sensu late, Boletales, Septobasidiales, Tilletiales, Uredinales and Ustilaginales. These sequences were analyzed together with additional GenBank sequences for three basidiomycetes, five ascomycetes, and a zygomycete, using methods of maximum likelihood, maximum parsimony and minimum-evolution. Using Mucor racemosus as an outgroup, the basidiomycetes analyzed under models of maximum likelihood and maximum parsimony formed nearly identical trees each composed of seven distinct clades: the smuts and bunts, a complex-septate group, two separate groups of auriculariaceous simple-septate species, the rusts and two unique branches each comprising a single taxon Agaricostilbum pulcherrimum and Cryptococcus neoformans. The minimum-evolution topology was different from the former two trees in the placement of the smuts and bunts with respect to the complex septate taxa, the position of Agaricostilbum pulcherrimum and the localized structure of the clade containing the taxa Eocronartium muscicola, Pachnocybe ferruginea and Septobasidium carestianum. Relative rate tests of nucleotide substitutions based on maximum likelihood estimations suggest significant evolutionary rate differences among the orders. To statistically differentiate among the different topologies, all trees were subjected to a likelihood variance test. Under assumptions of maximum likelihood, the test rejected the minimum-evolution tree but did not discriminate against any of the topologies generated by either maximum likelihood or maximum parsimony. These results suggest that the 5' end of the nuclear large subunit ribosomal DNA is useful for intergeneric comparisons of basidiomycetous fungi. The sequence data clarify the relationships among the genera of the Auriculariales sensu late and support the hypothesis that the Uredinales are a derived group.
