The genus Albatrellus is an important group of stipitate terrestrial fungi in the order Russulales. Some species in the genus form ectomycorrhizae, mostly with trees of Pinaceae; some are well-known edible mushrooms. However, its diversity and biogeography are unclear. Taxonomic and phylogenetic studies on Albatrellus were carried out by morphological examination, which included detailed observations of the fruiting body, spore shape and size, and other key features, together with potential hosts. These observations were then compared and analysed using multi-locus molecular phylogenetic analyses, including the internal transcribed spacer regions (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), the translation elongation factor 1-α gene (tef1), the largest subunit of RNA polymerase II (rpb1), the second largest subunit of RNA polymerase II (rpb2), the small subunit mitochondrial rRNA gene (mtSSU), and the small subunit of the nuclear ribosomal RNA gene (nucSSU). The results demonstrated that the species of Albatrellus formed eight clades. Nine new species are described and illustrated, and two new combinations are proposed. A total of 38 species are accepted in Albatrellus worldwide. Of those species, 26, 7, and 8 species are distributed in Asia, Europe, and North America, respectively. The divergence time indicated that the maximum crown age of Albatrellus was approximately 70.5 million years ago, and East Asia and North America are the likely ancestral areas. Dispersal and differentiation to other continents occurred during the late Paleocene and Miocene. Three kinds of dispersal routes are proposed: East Asia and Europe, East Asia and North America, and Europe and North America.

• Keywords
• Albatrellaceae, ectomycorrhizae, morphology, multi-gene phylogeny,
• Publication type
• Journal Article MeSH

The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.

• Keywords
• amplicon abundance, chimera, sympatric species, threshold,
• Publication type
• Journal Article MeSH

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

• Keywords
• Arctic biology, TE proliferation, biotrophy–saprotrophy evolution, carbon degradation, fungal genomics, fungal guild, genome size diversity, plant-fungus interactions, root-associations, saprotrophs,
• MeSH
• Agaricales * genetics   MeSH
• Phylogeny MeSH
• Genome, Fungal * genetics   MeSH
• Evolution, Molecular MeSH
• Gene Transfer, Horizontal MeSH
• Plants microbiology   genetics   MeSH
• DNA Transposable Elements genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA Transposable Elements MeSH

Haploporus species have a worldwide distribution and 27 species have been accepted. In this study, two new species, Haploporuscrystallinus and H.dextrinoideus, are proposed from South America, based on the molecular fragments (ITS, LSU and mtSSU) and morphological evidence. Molecular clock analysis was performed and the result suggests that the ancestor of Polyporales originated between the Late Jurassic and Early Cretaceous period, with a mean stem of 159.8 Mya [95% higher posterior density (HPD) of 142.4-184.1 Mya] and the genus Haploporus occurred at a mean stem of 108.3 Mya (95% HPD of 88.5-128.2 Mya). In addition, most species of the genus are diversified between 60.5 Mya and 1.8 Mya, during the Paleogene to Neogene. A key to the accepted species of the genus Haploporus is provided.

• Keywords
• fungal diversity, molecular clock dating, new taxa, wood-inhabiting fungi,
• Publication type
• Journal Article MeSH

Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.

• Keywords
• ABTS assay, basidiomycetes, diversity, gilled mushrooms, phylogeny,
• Publication type
• Journal Article MeSH

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.

• MeSH
• Basidiomycota * genetics   MeSH
• Wood microbiology   MeSH
• Fungal Proteins genetics   metabolism   MeSH
• Phylogeny MeSH
• Genome, Fungal MeSH
• Polyporales * genetics   metabolism   MeSH
• Transcriptome genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• Fungal Proteins MeSH

Russula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological range and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s. lat. represents a species complex consisting of at least five European, three North American, and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra complex is proposed and a key to the described European species of R. subgen. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta, and R. ustulata. Different thresholds of UNITE species hypotheses were tested against the taxonomic data. The distance threshold of 0.5% gives a perfect match to the phylogenetically defined species within the R. albonigra complex. Publicly available sequence data can contribute to species delimitation and increase our knowledge on ecology and distribution, but the pitfalls are short and low quality sequences.

• Keywords
• Basidiomycota, Coalescent species delimitation, Ectomycorrhizal fungi, Integrative taxonomy, New species, New taxa, Phylogeny, Russula subgen. Compactae, Russulaceae, Russulales, Typification,
• Publication type
• Journal Article MeSH

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

• MeSH
• Ecosystem MeSH
• Fungal Proteins genetics   MeSH
• Phylogeny MeSH
• Plant Physiological Phenomena MeSH
• Genome, Fungal * MeSH
• Fungi classification   genetics   physiology   MeSH
• Evolution, Molecular MeSH
• Mycorrhizae classification   genetics   physiology   MeSH
• Plants microbiology   MeSH
• Symbiosis * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• Fungal Proteins MeSH