An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences

In this study we provide a phylogenetically based introduction to the classes and orders of Pucciniomycotina (= Urediniomycetes), one of three subphyla of Basidiomycota. More than 8000 species of Pucciniomycotina have been described including putative saprotrophs and parasites of plants, animals and fungi. The overwhelming majority of these (approximately 90%) belong to a single order of obligate plant pathogens, the Pucciniales (= Uredinales), or rust fungi. We have assembled a dataset of previously published and newly generated sequence data from two nuclear rDNA genes (large subunit and small subunit) including exemplars from all known major groups in order to test hypotheses about evolutionary relationships among the Pucciniomycotina. The utility of combining nuc-lsu sequences spanning the entire D1-D3 region with complete nuc-ssu sequences for resolution and support of nodes is discussed. Our study confirms Pucciniomycotina as a monophyletic group of Basidiomycota. In total our results support eight major clades ranked as classes (Agaricostilbomycetes, Atractiellomycetes, Classiculomycetes, Cryptomycocolacomycetes, Cystobasidiomycetes, Microbotryomycetes, Mixiomycetes and Pucciniomycetes) and 18 orders.     

Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies

We sampled and analyzed approximately 2900bp across the three loci from 54 taxa belonging to a taxonomically difficult group of Cortinarius subgenus Phlegmacium. The combined analyses of ITS and variable regions of RPB1 and RPB2 greatly increase the resolution and nodal support for phylogenies of these closely related species belonging to clades that until now have proven very difficult to resolve with the ribosomal markers, nLSU and ITS. We present the first study of the utility of variable regions of the genes encoding the two largest subunits of RNA polymerase II (RPB1 and RPB2) for inferring the phylogeny of mushroom-forming fungi in combination with and compared to the widely used ribosomal marker ITS. The studied region of RPB1 contains an intron of the size and variability of ITS along with many variable positions in coding regions. Though almost entirely coding, the studied region of RPB2 is more variable than ITS. Both RNA polymerase II genes were alignable across all taxa. Our results indicate that several sections of Cortinarius need redefinition, and that several taxa treated at subspecific and varietal level should be treated at specific level. We suggest a new section for the two species, C. caesiocortinatus and C. prasinocyaneus, which constitute a well-supported separate lineage. We speculate that sequence information from RNA polymerase II genes have the potential for resolving phylogenetic problems at several levels of the diverse and taxonomically very challenging genus Cortinarius.     

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.     

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.     

Phylogenetic relationships of cyphelloid homobasidiomycetes

The homobasidiomycetes includes the mushroom-forming fungi. Members of the homobasidiomycetes produce the largest, most complex fruiting bodies in the fungi, such as gilled mushrooms ("agarics"), boletes, polypores, and puffballs. The homobasidiomycetes also includes species that produce minute, cup- or tube-shaped "cyphelloid" fruiting bodies, that rarely exceed 1-2 mm diameter. The goal of this study was to estimate the phylogenetic placements of cyphelloid fungi within the homobasidiomycetes. Sequences from the nuclear large subunit (nuc-lsu) ribosomal DNA (rDNA), 5.8S rDNA, and internal transcribed spacers (ITS) 1 and 2 were obtained for 31 samples of cyphelloid fungi and 16 samples of other homobasidiomycetes, and combined with published sequences. In total, 71 sequences of cyphelloid fungi were included, representing 16 genera. Preliminary phylogenetic analyses of a 1477-sequence data set and BLAST searches using sequences of cyphelloid forms as queries were used to identify taxa that could be close relatives of cyphelloid forms. Subsequent phylogenetic analyses of one data set with 209 samples represented by nuc-lsu rDNA sequences (analyzed with parsimony) and another with 38 samples represented by nuc-lsu and 5.8S rDNA sequences (analyzed with parsimony and maximum likelihood) indicated that cyphelloid forms represent a polyphyletic assemblage of reduced agarics (euagarics clade, Agaricales). Unconstrained tree topologies suggest that there have been about 10-12 origins of cyphelloid forms, but evaluation of constrained topologies with the Shimodaira-Hasegawa test suggests that somewhat more parsimonious scenarios cannot be rejected. Whatever their number, the multiple independent origins of cyphelloid forms represent striking cases of parallel evolutionary reduction of complex fungal morphology.     

Evolutionary relationships of Mycaureola dilseae (Agaricales), a basidiomycete pathogen of a subtidal rhodophyte

Mushroom-forming fungi (homobasidiomycetes) are major examples of morphological and ecological diversification in terrestrial habitats. Homobasidiomycetes includes only nine described species that are known from marine environments. Morphological traits that have concealed the ancestry of these fungi include reduced fruiting bodies with hairy surfaces and extremely modified spores, both of which may function as floating devices to aid successful dispersal and adhesion to various substrates such as driftwood. Our previous results suggested that all marine forms as yet investigated are placed in the Nia clade (euagarics) and that they have primarily evolved from cypelloid forms (minute, cup-shaped, terrestrial saprotrophs) via transitions through mangroves to fully marine habitats. We show here that Mycaureola dilseae, which parasitizes the red alga Dilsea carnosa, is a second independent lineage of marine fungi in the euagarics clade that is not related to cyphelloid forms. Phylogenetic reconstructions were based on two data sets: a partial four-region rDNA data set (nuc-ssu, nuc-lsu, mt-ssu, and mt-lsu) with inclusive sampling of 249 taxa and a densely sampled ITS data set including 32 taxa, which formed a clade with Mycaureola in the four-region rDNA analyses. Inferences using constrained and unconstrained six-parameter weighted parsimony, Bayesian Markov chain Monte Carlo methods, and maximum likelihood approaches place M. dilseae in the morphologically diverse /physalacriaceae clade next to Gloiocephala spp., a group of highly reduced stipitate-pileate saprotrophs.