Phylogenetic relationships in <i>Ganoderma</i> inferred from the internal transcribed spacers and 25S ribosomal DNA sequences

Over 250 species have been described in Ganoderma. Species identification and species circumscription are often unclear and taxonomic segregation of the genus remains controversial. In this study we sequenced the 5′ half of the 25S ribosomal RNA gene and the internal transcribed spacers to determine appropriate regions to i) discriminate between Ganoderma species and ii) infer taxonomic segregation of Ganoderma s. lato (Ganodermataceae) on a phylogenetic basis. We studied 19 Ganoderma isolates representing 14 species classified in 5 subgenera and sections, one isolate of the related genus Amauroderma, and one isolate of Fomitopsis which served as the out- group in parsimony analysis. Results showed that a transition bias was present in our data, and that rates of nucleotide divergence in the different ribosomal regions varied between lineages. Independent and combined analyses of different data sets were performed and results were discussed. Nucleotide sequences of the internal transcribed spacers, but not those of the coding regions, distinguished between most Ganoderma species, and indicated that isolates of the G. tsugae group were misnamed. Phylogenetic analysis of the combined data sets of the divergent domain D2 of the 25S ribosomal RNA gene and of the internal transcribed spacers indicated that subgenus Elfvingia was monophyletic, whereas sections Characoderma and Phaeonema were not. Combined data from these regions is useful for infrageneric segregation of Ganoderma on a phylogenetic basis. Phylogenetic analysis from data of the D2 region alone strongly supported Amauroderma as a sister taxon of Ganoderma. This suggested that the D2 region should be suitable for systematics at higher taxonomic ranks in the Ganodermataceae. The low sequence variation observed in the 25S ribosomal gene within Ganoderma species suggested that the genus is young.