Higher-level phylogenetic relationships of Homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions.

Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among these clades. A dataset of 93 species that represent all eight previously recognized clades was assembled, with 3800 bp of sequence data from nuclear and mitochondrial large and small subunit rDNAs for each taxon. Parsimony and maximum-likelihood analyses support the monophyly of the eight major clades recognized by Hibbett and Thorn. Most groups are strongly supported in bootstrapped parsimony analyses, but the polyporoid clade remains weakly supported. For the first time, the sister-group relationship of the euagarics clade and bolete clade is strongly supported, and the Hygrophoraceae is strongly supported as the sister group of the rest of the euagarics clade. Nevertheless, the backbone of the homobasidiomycete phylogeny, and the internal structure of several clades, remain poorly resolved.     

Is Phellinites digiustoi the oldest homobasidiomycete?

The oldest generally accepted fossil of mushroom-forming fungi (homobasidiomycetes) is Phellinites digiustoi, from the Jurassic of Patagonia. The next-oldest homobasidiomycete fossil does not occur until about 70 million years later, in the mid-Cretaceous. The goal of this project was to reassess the identity of Phellinites and refine the minimum-age estimate for the origin of homobasidiomycetes. We examined the holotype of Phellinites digiustoi and a second collection from the type locality. Thin sections were prepared from both collections. Phellinites has a cellular structure, confirming that it is biological in origin, but there are no hyphae, spores, or other fungal structures. Rather, Phellinites appears to be the outer bark (rhytidome) of a conifer. Fossils of Araucariaceae are common in the region where Phellinites was found, and so it is plausible that Phellinites is the bark of an Araucaria-like tree. The minimum age of the mushroom-forming fungi, based on direct fossil evidence, is revised to the mid-Cretaceous.     

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.     

Evolution of complex fruiting-body morphologies in homobasidiomycetes

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes.     

A new lineage of lichenized basidiomycetes inferred from a two-gene phylogeny: The Lepidostromataceae with three species from the tropics

The lichen habit has apparently evolved independently in at least five major clades of mushroom-forming basidiomycetes (Agaricomycetes). Tracing the origin of lichenization in these groups depends on a clearer understanding of the phylogenetic relationships of basidiolichens to other fungi. We describe here a new family of basidiolichens made up of tropical, soil-inhabiting fungi that form lichenized, scale-like squamules and erect, coral-like fruiting structures. These structures are common to two basidiolichen genera, Multiclavula and Lepidostroma. Molecular studies have confirmed the phylogenetic position of Multiclavula species in the Cantharellales, but Lepidostroma species have never been sequenced. We obtained nuclear small and large subunit ribosomal sequences from specimens of L. calocerum collected in Costa Rica and Mexico and also from specimens of two Multiclavula spp. recently described from Rwanda. The phylogenetic placement of these fungi within the Agaricomycetes was investigated using likelihood and Bayesian analyses. Our results indicate that L. calocerum and the Rwandan species form a natural group unrelated to Multiclavula and sister to the Atheliales, members of which are neither lichen-forming nor clavarioid. The independent evolution of morphologically similar forms in so many groups of basidiomycetes is a remarkable example of convergence, indicating similar pathways to lichenization in these fungi.     

Lichenicolous fungi are more specialized than their lichen hosts in primeval forest ecosystems,Białowieża Forest,northeast Poland

Taxonomy and diversity of symptomatic lichenicolous fungi (visible as fruitbodies on lichen thalli, their discoloration, and/or deformation) and their specificity to lichen hosts is becoming more and more studied. However, information on their ecology is still scarce. We assess how large the specialization of these fungi towards their hosts and microhabitat is. Epiphytic, epixylic and epigeic lichens and associated lichenicolous fungi were studied on 144 permanent plots in Białowieża Forest in relation to forest communities, species of tree phorophyte and substrates. On all these three studied levels lichenicolous fungi were more specialized than their lichen hosts. Our study provides the first estimation of ecological dependences between associations of lichenicolous fungi and their hosts, microhabitats and forest communities in a primeval forest ecosystem representative of lowland Europe.     

Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi

Group I introns were discovered inserted at the same position in the nuclear small-subunit ribosomal DNA (nuc-ssu-rDNA) in several species of homobasidiomycetes (mushroom-forming fungi). Based on conserved intron sequences, a pair of intron-specific primers was designed for PCR amplification and sequencing of intron-containing rDNA repeats. Using the intron-specific primers together with flanking rDNA primers, a PCR assay was conducted to determine presence or absence of introns in 39 species of homobasidiomycetes. Introns were confined to the genera Panellus, Clavicorona, and Lentinellus. Phylogenetic analyses of nuc-ssu-rDNA and mitochondrial ssu-rDNA sequences suggest that Clavicorona and Lentinellus are closely related, but that Panellus is not closely related to these. The simplest explanation for the distribution of the introns is that they have been twice independently gained via horizontal transmission, once on the lineage leading to Panellus, and once on the lineage leading to Lentinellus and Clavicorona. BLAST searches using the introns from Panellus and Lentinellus as query sequences retrieved 16 other similar group I introns of nuc-ssu-rDNA and nuclear large-subunit rDNA (nuc-lsu-rDNA) from fungal and green algal hosts. Phylogenetic analyses of intron sequences suggest that the mushroom introns are monophyletic, and are nested within a clade that contains four other introns that insert at the same position as the mushroom introns, two from different groups of fungi and two from green algae. The distribution of host lineages and insertion sites among the introns suggests that horizontal and vertical transmission, homing, and transposition have been factors in intron evolution. As distinctive, heritable features of nuclear rDNAs in certain lineages, group I introns have promise as phylogenetic markers. Nevertheless, the possibility of horizontal transmission and homing also suggest that their use poses certain pitfalls.      

The obligately lichenicolous genus Lichenoconium represents a novel lineage in the Dothideomycetes

Lichenicolous fungi are obligately lichen-associated organisms that have evolved many times throughout the Ascomycota and Basidiomycota. Approximately 20% of lichenicolous ascomycetes are recognized only from asexual (anamorphic) characteristics, so the phylogenetic position of many groups has never been resolved. Here we present the first molecular phylogeny of Lichenoconium, a genus of strictly asexual, obligately lichenicolous species with broad geographic distributions and diverse host ecologies. We obtained nuclear and mitochondrial rDNA sequences from fungal cultures isolated from four species in the genus, including a new species, Lichenoconium aeruginosum sp. nov., collected in France, Luxembourg and Netherlands. Our multilocus phylogeny supports the monophyly of fungi in the genus Lichenoconium, and places the genus in the Dothideomycetes, an ascomycete class made up mainly of saprobes and plant-associated endophytes and pathogens. There are only a few recognized groups of lichen-formers in the Dothideomycetes, but Lichenoconium is not supported as being closely related to any of these, nor to any other recognized order within the Dothideomycetes. Given that Lichenoconium is but one of over 100 genera of anamorphic lichenicolous fungi, most of which have never been studied phylogenetically, we suggest that asexual lichenicolous fungi may represent novel and evolutionarily significant phylogenetic groups in the Kingdom Fungi.     

Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales)

Approximately 3000 bp across 84 taxa have been analyzed for variable regions of RPB1, RPB2, and nLSU-rDNA to infer phylogenetic relationships in the large ectomycorrhizal mushroom genus Inocybe (Agaricales; Basidiomycota). This study represents the first effort to combine variable regions of RPB1 and RPB2 with nLSU-rDNA for low-level phylogenetic studies in mushroom-forming fungi. Combination of the three loci increases non-parametric bootstrap support, Bayesian posterior probabilities, and resolution for numerous clades compared to separate gene analyses. These data suggest the evolution of at least five major lineages in Inocybe-the Inocybe clade, the Mallocybe clade, the Auritella clade, the Inosperma clade, and the Pseudosperma clade. Additionally, many clades nested within each major lineage are strongly supported. These results also suggest the family Crepiodataceae sensu stricto is sister to Inocybe. Recognition of Inocybe at the family level, the Inocybaceae, is recommended.     

Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)

The Tremellomycetes (Agaricomycotina, Basidiomycota, Fungi) are a nutritionally heterogeneous group comprising saprotrophs, animal parasites, and fungicolous species (fungal-inhabiting, including lichen-inhabiting). The relationships of many species, particularly those with a lichenicolous habit, have never been investigated by molecular methods. We present a phylogeny of the Tremellomycetes based on three nuclear DNA ribosomal markers (nSSU, 5.8S and nLSU), representing all main taxonomic groups and life forms, including lichenicolous taxa. The Cystofilobasidiales, Filobasidiales, Holtermanniales, and Tremellales (including the Trichosporonales) are recovered as monophyletic, but this is not the case for the Tremellomycetes. We suggest, however, that the Cystofilobasidiales tentatively continue to be included in the Tremellomycetes. As currently circumscribed, the Filobasidiaceae, Sirobasidiaceae, Syzygosporaceae and Tremellaceae are non-monophyletic. Cuniculitremaceae, Sirobasidiaceae and Tetragoniomycetaceae are nested within Tremellaceae. The lichenicolous species currently included within the Tremellomycetes belong in this group, distributed across the Filobasidiales and Tremellales. Lichen-inhabiting taxa do not form a monophyletic group; they are distributed in several clades and sometimes intermixed with taxa of other nutritional habits. Character state reconstruction indicates that two morphological traits claimed to characterize groups in the Tremellomycetes (the basidium habit and basidium septation) are highly homoplastic. Comparative phylogenetic methods suggest that the transitions between single and catenulate basidia in the Tremellales are consistent with a punctuational model of evolution whereas basidium septation is likely to have evolved under a graduational model in the clade comprising the Holtermanniales, Filobasidiales, and Tremellales.     

One hundred and seventeen clades of euagarics

This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5(') end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.     

Radiation of mushroom-forming fungi correlates with novel modes of protecting sexual fruiting bodies

The protection of vulnerable developing structures evolved repeatedly in terrestrial organisms and includes, among others, viviparity in animals and the seed in land plants. In mushroom-forming fungi (Agaricomycetes), sexual spores are born on fruiting bodies, the growth of which is a complex developmental process that is exposed to environmental factors (e.g., desiccation, fungivorous animals). Mushroom-forming fungi evolved a series of innovations in fruiting body protection, however, how these emerged is obscure, leaving the evolutionary principles of fruiting body development poorly known. Here, we show that developmental innovations that lead to the spore-producing surface (hymenophore) being enclosed in a protected environment display asymmetry in their evolution and are associated with increased diversification rates. ‘Enclosed’ development evolved convergently and became a dominant developmental type in several clades of mushrooms. This probably mirrors spore production benefits for species with protected fruiting body initials, by better coping with environmental factors. Our observations highlight new morphological traits associated with mushroom diversification that parallel the evolution of protection strategies in other organisms, such as viviparity or the seed in animals or plants, respectively, but in the context of spore development, highlighting the general importance of protecting vulnerable progeny across the tree of life.     

Effects of gasteroid fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis

Gasteroid fungi include puffballs, stinkhorns, and other forms that produce their spores inside the fruiting body. Gasteroid taxa comprise about 8.4% of the Agaricomycetes (mushroom-forming fungi) and have evolved numerous times from nongasteroid ancestors, such as gilled mushrooms, polypores, and coral fungi, which produce spores on the surface of the fruiting body. Nongasteroid Agaricomycetes have a complex mechanism of forcible spore discharge that is lost in gasteroid lineages, making reversals to nongasteroid forms very unlikely. Our objective was to determine whether gasteromycetation affects the rate of diversification of lineages "trapped" in the gasteroid state. We assembled four datasets (the Sclerodermatineae, Boletales, Phallomycetidae, and Lycoperdaceae), representing unique origins of gasteroid fungi from nongasteroid ancestors and generated phylogenies using BEAST. Using the program Diversitree, we analyzed these phylogenies to estimate character-state-specific rates of speciation and extinction, and rates of transitions between nongasteroid and gasteroid forms. Most optimal models suggest that the net diversification rate of gasteroid forms exceeds that of nongasteroid forms, and that gasteroid forms will eventually come to predominate over nongasteroid forms in the clades in which they have arisen. The low frequency of gasteroid forms in the Agaricomycetes as a whole may reflect the recent origins of many gasteroid lineages.     

<Emphasis Type="Italic">Endohyalina</Emphasis>, the genus in the Physciaceae to accommodate the species of the <Emphasis Type="Italic">Rinodina ericina-</Emphasis>group

The genus Endohyalina is characterized by crustose, autonomous, or obligately lichenicolous thalli, lecideine apothecia with a hymenium often more or less inspersed with oil droplets and a brown hypothecium, Bacidia-type asci, small Dirinaria-type ascospores developing with type B ontogeny, bacilliform conidia and containing diploicin as the major secondary metabolite. The genus is based on four species previously included in Rinodina—R. ericina s. lat., R. insularis, R. interjecta and R. kalbii—and on two lichenicolous species from the Canary Islands described here as new, Endohyalina brandii and E. diederichii. The generic type, Endohyalina rappii, is reduced to synonymy with E. ericina whereas E. circumpallida is excluded from the genus and returned to Buellia s. lat. Except for the thalline growth form and the common lichenicolous habit, the diagnostic characters of Endohyalina are akin to those of Diploicia. New chemical data on Endohyalina insularis and E. kalbii are reported, and a simple method for determining the secondary chemistry of lichenicolous fungi is provided.     

Perspectives in the new Russulales

The Russulales is one of 12 major lineages recently elucidated by molecular sequence data in the homobasidiomycetes. The order is morphologically most diverse, containing a remarkable variety of sporophore forms including resupinate, discoid, effused-reflexed, clavarioid, pileate, or gasteroid and hymenophore configurations from smooth, poroid, hydnoid, lamellate, to labyrinthoid. Functionally these fungi are primarily saprotrophs but others are ectomycorrhizal, root parasites and insect symbionts. A phylogenetic analysis of the nuclear 5.8S, ITS2 and large-subunit rDNA genes comprises the best information to date on relationships of taxa within the Russulales. Two large sister groups encompassing 11-13 major clades have been recovered within the Russulales. Based on molecular and morphological data 12 families and approximately 80 genera have been identified, although placement of many taxa has not yet been determined. The two clades containing ectomycorrhizal taxa, corresponding to the Russulaceae and the Albatrellaceae, represent the greatest diversity of sporophore morphologies. The primarily pileate lamellate family Russulaceae is nested with resupinate species and also contains pileate sequestrate, gasteroid annulate and pleurotoid forms. Albatrellaceae similarly contains resupinate poroid, pileate poroid and pileate labyrinthoid sporophores. Presence of gloeoplerous hyphae containing fluid that typically stains black in sulfoaldehyde compounds is a synapomorphy for the Russulales. Amyloid reactions in spore or hyphal walls that occur frequently throughout the Russulales often are perceived as an obvious synapomorphy but are inconsistent. Approaches including sequencing functional genes, analysis of gene expression and biochemical analysis across the entire order are needed.     

ITS2 metabarcoding analysis complements lichen mycobiome diversity data

Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.     

整合转录组数据鉴定大型真菌原基形成的潜在通路

[背景]大型真菌子实体发育特别是从菌丝体到原基转变的分子机制,目前仍不清楚.现有的研究大多集中在有限的真菌种类或环境因素上,但对在发育中起关键作用的基因提供的信息有限.[目的]研究大型真菌原基形成的分子机制.[方法]对11个物种及4个环境因子相关的转录组数据进行分析.[结果]与对照组相比,上调基因数量从白灵菇(Pleu...     

Sexual selection in mushroom-forming basidiomycetes

We expect that sexual selection may play an important role in the evolution of mushroom-forming basidiomycete fungi. Although these fungi do not have separate sexes, they do play female and male roles: the acceptance and the donation of a nucleus, respectively. The primary mycelium (monokaryon) of basidiomycete fungi, growing from a germinating sexual spore, is hermaphroditic, but it loses female function upon the acceptance of a second nucleus. The resulting dikaryon with two different nuclei in each cell retains a male potential as both nuclei can fertilize receptive mycelia. We tested the occurrence of sexual selection in the model species of mushroom-forming basidiomycetes, Schizophyllum commune, by pairing monokaryons with fully compatible dikaryons. In most pairings, we found a strong bias for one of the two nuclei although both were compatible with the monokaryon when paired alone. This shows that sexual selection can occur in mushroom-forming basidiomycetes. Since the winning nucleus of a dikaryon occasionally varied depending on the receiving monokaryon, we infer that sexual selection can operate through choosiness of the receiving individual (analogous to female choice). However, in other cases the same nucleus won, irrespective of the receiving monokaryon, suggesting that competition between the two nuclei of the donating mycelium (analogous to male–male competition) might also play a role.     

After the gold rush,or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century

Mushroom-forming fungi (Agaricomycetes, approx. syn.: Homobasidiomycetes) produce a diverse array of fruiting bodies, ranging from simple crust-like forms to complex, developmentally integrated forms, such as stinkhorns and veiled agarics. The 19th century Friesian system divided the mushroom-forming fungi according to macromorphology. The Friesian taxonomy has long been regarded as artificial, but it continues to influence the language of mycology and perceptions of fungal diversity. Throughout the 20th century, the phylogenetic significance of anatomical features was elucidated, and classifications that departed strongly from the Friesian system were proposed. However, the anatomical studies left many questions and controversies unresolved, due in part to the paucity of characters, as well as the general absence of explicit phylogenetic analyses. Problems in fruiting body evolution were among the first to be addressed when molecular characters became readily accessible in the late 1980s. Today, GenBank contains about 108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names. Analyses of these data are providing an increasingly detailed and robust view of the phylogeny and the distribution of different fruiting body forms across the 14 major clades that make up the agaricomycetes. However, it would be wrong to suggest that all the important questions about fruiting body evolution have been resolved. Recent studies focusing on resupinate forms suggest that there may still be undetected major clades of agaricomycetes, which could have a significant impact on our estimates of the ancestral forms in this morphologically diverse group. Modern approaches, including comparative phylogenetic analyses and developmental studies, have the potential to yield novel insights into both the macroevolutionary processes and cellular mechanisms of fungal morphological evolution.