Major clades of Agaricales: a multilocus phylogenetic overview

Abstract

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.

Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution

“…Current molecular data support its separation from Hygrocybe ( Matheny et al 2006). Basidiocarps of Camarophyllus have decurrent lamellae, white or cream spore print, and predominantly white or brownish-orange colors.…”

“…This species has been reported from North America and China, on soil under conifers or broad-leaved trees (Bi et al 1993;Bigelow & Smith 1973). Cantharocybe was described as 'apparently saprotrophic', though to this day uncertainty remains about its trophic strategy ( Matheny et al 2006). There is no obvious morphological connection between Cantharocybe and Volvariella.…”

“…In order to find unidentified environmental samples potentially belonging to Pluteus or Volvariella, all newly generated ITS sequences were used for BLAST searches (http://blast.ncbi.nlm.nih.gov/Blast.cgi), yielding seven additional sequences of Pluteus that were included in the ITS dataset. Genbank sequences, for taxa other than Pluteus and Volvariella, employed in the combined nSSU + ITS + nLSU datasets, are the same ones used in the study of Matheny et al (2006). Accession numbers for the sequences used in the nLSU analysis are given on the tree (Fig 2).…”

“…and Schizophyllum Fr. Matheny et al (2006) presented the results of a six gene phylogeny of the Agaricales, including three taxa of Pluteus, one of Volvariella (V. gloiocephala) and one of Melanoleuca. In this analysis Pluteus appears as monophyletic with V. gloiocephala as its sister group, and Melanoleuca closely related.…”

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”