The order Agaricales was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and delimitations of some taxa, such as Sarcomyxaceae and Tricholomopsis, remain unsettled. In this study, sequence data of 38 genomes were generated through genome skimming on an Illumina sequencing system. To anchor the systematic position of Sarcomyxaceae and Tricholomopsis, a phylogenetic analysis based on 555 single-copy orthologous genes from the aforementioned genomes and 126 publicly accessible genomes was performed. The results fully supported the clustering of Tricholomopsis with Phyllotopsis and Pleurocybella within Phyllotopsidaceae, which formed a divergent monophyletic major lineage together with Pterulaceae, Radulomycetaceae, and Macrotyphula in Agaricales. The analysis also revealed that Sarcomyxaceae formed a unique major clade. Therefore, two new suborders, Phyllotopsidineae and Sarcomyxineae, are proposed for the two major lineages. Analyses of 450 single-copy orthologous genes and four loci suggested that Tricholomopsis consisted of at least four clades. Tricholomopsis is subsequently subdivided into four distinct sections. Seventeen Tricholomopsis species in China, including six new species, are reported. Conoloma is established to accommodate T. mucronata. The substrate preference of Tricholomopsis species and the transitions of the pileate ornamentations among the species within the genus are discussed.

“Lingzhi” is a fungus found in China for about 2000 years, renowned for its immense values in traditional Chinese medicine and culture. This fungus was generally assigned to Ganoderma lucidum, a species originally described from the UK. In the mid-nineties of the twentieth century, molecular phylogenetic analyses indicated that collections named G. lucidum in East Asia were in most cases not conspecific with G. lucidum found in Europe. However, the scientific name for the “lingzhi” found in China remained unclarified ever since. To clarify the identity of this fungus, two groups of Chinese mycologists have simultaneously gathered morphological and molecular evidence. One group concluded that “lingzhi” belonged to G. sichuanense, a species which was collected from Sichuan, a province in southwestern China, while the other group stated that the “lingzhi” is an undescribed species and, thus, named it as G. lingzhi. Our molecular phylogenetic evidence showed that G. lucidum s. str. occurs not only in northwestern and northeastern China but also in the highlands of southwestern China, where it has been commercially cultivated. In other words, both G. lucidum s. str. and G. lingzhi occur in natural environments in China, where they have been cultivated. Due to the phenotypic plasticity and morphological stasis, DNA sequence data play a vital role in characterizing the species within the G. lucidum-complex. Because the internal transcribed spacer (ITS) sequence has been successfully generated only once from the holotype of G. sichuanense, it suggests that the DNA in the holotype might have been largely digested. To settle the disputation and to clarify the relationships and taxonomic issues among G. lingzhi, G. sichuanense, G. sinense and other species in the complex, an epitype for G. sichuanense and for G. sinense from their type locality should be selected, and nucleotide sequences of more informative DNA markers should be used to delimit the species in the complex in the near future. In view of its economic, medicinal and cultural importance, the widely cultivated G. lingzhi is nominated as the fungus of the year (2013) for the journal Mycology.