Phylogeny, divergence time estimation, and biogeography of the genus Heterobasidion (Basidiomycota, Russulales)

Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.

The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered

Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia and Fomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + TEF1, ITS + TEF1 + RPB1 and ITS + TEF1 + RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided. Taxonomic novelties: New species: Fomitopsis algumicola Grebenc & Spirin, F. caseosa Vlasák & Spirin, F. cupressicola Vlasák, J. Vlasák Jr. & Spirin, F. derelicta Vlasák & Spirin, F. dollingeri Vlasák & Spirin, F. fissa Vlasák & Spirin, F. lapidosa Miettinen & Spirin, F. lignicolor Vlasák & Spirin, F. maculosa Miettinen & Spirin, F. pannucea Runnel & Spirin, F. perhiemata Viner & Spirin, F. purpurea Spirin & Ryvarden, F. retorrida Spirin & Kotiranta, F. solaris Rivoire, A.M. Ainsworth & Vlasák, F. tristis Miettinen & Spirin, F. tunicata Miettinen & Spirin, F. visenda Miettinen & Spirin. New combinations: Fomitopsis aculeata (Cooke) Spirin & Miettinen, F. aethalodes (Mont.) Spirin, F. alaskana (D.V. Baxter) Spirin & Vlasák, F. albidoides (A. David & Dequatre) Bernicchia & Vlasák, F. amygdalina (Berk. & Ravenel) Spirin & Vlasák, F. angusta (Spirin & Vlasák) Spirin & Vlasák, F. atypa (Lév.) Spirin & Vlasák, F. caespitosa (Murrill) Spirin & Miettinen, F. calcitrosa (Spirin & Miettinen) Spirin & Miettinen, F. circularis (B.K. Cui & Hai J. Li) Spirin, F. concentrica (G. Cunn.) M.D. Barrett, F. cyclopis (Miettinen & Spirin) Miettinen & Spirin, F. dickinsii (Berk. ex Cooke) Spirin, F. elevata (Corner) Spirin & Miettinen, F. eucalypti (Kalchbr.) Spirin, F. ferrea (Cooke) Spirin & Viner, F. flavimontis (Vlasák & Spirin) Vlasák & Spirin, F. foedata (Berk.) Spirin & Miettinen, F. gilvidula (Bres.) Spirin & Miettinen, F. glabricystidia (Ipulet & Ryvarden) Miettinen & Ryvarden, F. globispora (Ryvarden & Aime) Spirin, F. hartmannii (Cooke) M.D. Barrett & Spirin, F. hyalina (Spirin, Miettinen & Kotir.) Spirin & Miettinen, F. hypoxantha (Bres.) Spirin & Miettinen, F. incana (Lév.) Spirin & V. Malysheva, F. infirma (Renvall & Niemelä) Miettinen & Niemelä, F. juniperina (Murrill) Spirin & Vlasák, F. kuzyana (Pilát ex Pilát) Spirin & Vlasák, F. leioderma (Mont.) Spirin & Vlasak, F. leucaena (Y.C. Dai & Niemelä) Spirin & Miettinen, F. luzonensis (Murrill) Spirin & Miettinen, F. maculatissima (Lloyd) Spirin, F. madronae (Vlasák & Ryvarden) Vlasák & Ryvarden, F. malicola (Berk. & M.A. Curtis) Spirin, F. marchionica (Mont.) Spirin & Miettinen, F. marianii (Bres.) Spirin, Vlasák & Cartabia, F. mellita (Niemelä & Penttilä) Niemelä & Miettinen, F. microcarpa (B.K. Cui & Shun Liu) Spirin, F. micropora (B.K. Cui & Shun Liu) Spirin, F. modesta (Kuntze ex Fr.) Vlasák & Spirin, F. monomitica (Yuan Y. Chen) Spirin & Viner, F. morganii (Lloyd) Spirin & Vlasák, F. moritziana (Lév.) Spirin & Miettinen, F. neotropica (D.L. Lindner, Ryvarden & T.J. Baroni) Vlasák, F. nigra (Berk.) Spirin & Miettinen, F. nivosella (Murrill) Spirin & Vlasák, F. oboensis (Decock, Amalfi & Ryvarden) Spirin, F. oleracea (R.W. Davidson & Lombard) Spirin & Vlasák, F. philippinensis (Murrill) Spirin & Vlasák, F. primaeva (Renvall & Niemelä) Miettinen & Niemelä, F. psilodermea (Berk. & Mont.) Spirin & Vlasák, F. pulverulenta (Rivoire) Rivoire, F. pulvina (Pers.) Spirin & Vlasák, F. pulvinascens (Pilát ex Pilát) Niemelä & Miettinen, F. quercina (L.) Spirin & Miettinen, F. ramentacea (Berk. & Broome) Spirin & Vlasák, F. renehenticii (Rivoire, Trichies & Vlasák) Rivoire & Vlasák, F. roseofusca (Romell) Spirin & Vlasák, F. sagraeana (Mont.) Vlasák & Spirin, F. sandaliae (Bernicchia & Ryvarden) Bernicchia & Vlasák, F. sclerotina (Rodway) M.D. Barrett & Spirin, F. serialiformis (Kout & Vlasák) Vlasák, F. serialis (Fr.) Spirin & Runnel, F. serrata (Vlasák & Spirin) Vlasák & Spirin, F. squamosella (Bernicchia & Ryvarden) Bernicchia & Ryvarden, F. stereoides (Fr.) Spirin, F. subectypa (Murrill) Spirin & Vlasák, F. substratosa (Malençon) Spirin & Miettinen, F. tropica (B.K. Cui) Spirin, F. tumulosa (Cooke) M.D. Barrett & Spirin, F. tuvensis (Spirin, Vlasák & Kotir.) Spirin & Vlasák, F. uralensis (Pilát) Spirin & Miettinen, F. ussuriensis (Bondartsev & Ljub.) Spirin & Miettinen, F. variiformis (Peck) Vlasák & Spirin, F. yunnanensis (M.L. Han & Q. An) Spirin, Daedaleopsis candicans (P. Karst.) Spirin, Megasporoporia eutelea (Har. & Pat.) Spirin & Viner, Neofomitella hemitephra (Berk.) M.D. Barrett, Pseudophaeolus soloniensis (Dubois) Spirin & Rivoire, P. trichrous (Berk. & M.A. Curtis) Vlasák & Spirin. New synonyms: Antrodia bondartsevae Spirin, A. huangshanensis Y.C. Dai & B.K. Cui, A. taxa T.T. Chang & W.N. Chou, A. wangii Y.C. Dai & H.S. Yuan, Antrodiella subnigra Oba, Mossebo & Ryvarden, Antrodiopsis Audet, Boletus quercinus Schrad., Brunneoporus Audet, Buglossoporus Kotl. & Pouzar, Buglossoporus eucalypticola M.L. Han, B.K. Cui & Y.C. Dai, Caloporus P. Karst., Cartilosoma Kotlaba & Pouzar, Coriolus clemensiae Murrill, C. cuneatiformis Murrill, C. hollickii Murrill, C. parthenius Hariot & Pat., C. rubritinctus Murrill, Daedalea Pers., Daedalea allantoidea M.L. Han, B.K. Cui & Y.C. Dai, D. americana M.L. Han, Vlasák & B.K. Cui, D. radiata B.K. Cui & Hai J. Li, D. rajchenbergiana Kossmann & Drechsler-Santos, D. sinensis Lloyd, Daedalella B.K. Cui & Shun Liu, Dentiporus Audet, Flavidoporia Audet, Fomes subferreus Murrill, Fomitopsis cana B.K. Cui, Hai J. Li & M.L. Han, F. caribensis B.K. Cui & Shun Liu, F. cystidiata B.K. Cui & M.L. Han, F. ginkgonis B.K. Cui & Shun Liu, F. iberica Melo & Ryvarden, F. incarnata K.M. Kim, J.S. Lee & H.S. Jung, F. subfeei B.K. Cui & M.L. Han, F. subtropica B.K. Cui & Hai J. Li, Fragifomes B.K. Cui, M.L. Han & Y.C. Dai, Leptoporus epileucinus Pilát, Melanoporia Murrill, Neoantrodia Audet, Neolentiporus Rajchenb., Nigroporus macroporus Ryvarden & Iturr., Niveoporofomes B.K. Cui, M.L. Han & Y.C. Dai, Pilatoporus Kotl. & Pouzar, Piptoporus P. Karst., Polyporus aurora Ces., P. durescens Overh. ex J. Lowe, P. griseodurus Lloyd, Poria incarnata Pers., Pseudoantrodia B.K. Cui, Y.Y. Chen & Shun Liu, Pseudofomitopsis B.K. Cui & Shun Liu, Ranadivia Zmitr., Rhizoporia Audet, Rhodofomes Kotl. & Pouzar, Rhodofomitopsis B.K. Cui, M.L. Han & Y.C. Dai, Rhodofomitopsis pseudofeei B.K. Cui & Shun Liu, R. roseomagna Nogueira-Melo, A.M.S. Soares & Gibertoni, Rubellofomes B.K. Cui, M.L. Han & Y.C. Dai, Subantrodia Audet, Trametes fulvirubida Corner, T. lignea Murrill, T. lusor Corner, T. pseudodochmia Corner, T. subalutacea Bourdot & Galzin, T. supermodesta Ryvarden & Iturr., T. tuberculata Bres., Tyromyces multipapillatus Corner, T. ochraceivinosus Corner, T. palmarum Murrill, T. singularis Corner, T. squamosellus Núñez & Ryvarden, Ungulidaedalea B.K. Cui, M.L. Han & Y.C. Dai. Lectotypes: Hexagonia sulcata Berk., Polyporus castaneae Bourdot & Galzin, Poria incarnata Pers., Trametes subalutacea Bourdot & Galzin, Ungulina substratosa Malençon. Neotypes: Agaricus soloniensis Dubois, Boletus pulvinus Pers. Citation: Spirin V, Runnel K, Vlasák J, Viner I, Barrett MD, Ryvarden L, Bernicchia A, Rivoire B, Ainsworth AM, Grebenc T, Cartabia M, Niemelä T, Larsson K-H, Miettinen O (2024). The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered. Studies in Mycology 107: 149-249. doi: 10.3114/sim.2024.107.03.

Outline, phylogenetic and divergence times analyses of the genus Haploporus (Polyporales, Basidiomycota): two new species are proposed

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.

Taxonomy and phylogeny of Sidera (Hymenochaetales, Rickenella clade) from China and North America revealing two new species

Sidera, belonging to the Rickenella clade of Hymenochaetales, is a worldwide genus with mostly poroid hymenophore of wood-inhabiting fungi. Two new species in the genus, Sideraamericana and S.borealis, are described and illustrated from China and North America based on morphological and molecular evidence. They were mainly found growing on rotten wood of Abies, Picea and Pinus. S.americana is characterized by annual, resupinate basidiomata with silk sheen when dry, round pores (9-11 per mm), a dimitic hyphal system, and allantoid basidiospores measuring 3.5-4.2 × 1 μm. S.borealis is characterized by annual, resupinate basidiomata with cream to pinkish buff dry pore surface, angular pores (6-7 per mm), a dimitic hyphal system, and allantoid basidiospores measuring 3.9-4.1 × 1-1.1 μm. Phylogenetic analysis based on a combined 2-locus dataset [ITS1-5.8S-ITS2 (ITS) + nuclear large subunit RNA (nLSU)] shows that the two species are members of Sidera, and they are compared with morphologically similar and phylogenetically related species, respectively. An identification key to 18 accepted species of Sidera in worldwide is provided.

Climacocystaceae fam. nov. and Gloeoporellaceae fam. nov., two new families of Polyporales (Basidiomycota)

Polyporales is a diverse group of Agaricomycetes including more than 2,500 species belonging to 255 genera and 18 families. Recently, many studies focused on the classification of Polyporales, but the familial placements of some taxa remain uncertain. In this study, two new families, Climacocystaceae and Gloeoporellaceae of Polyporales, are proposed based on morphological characters and molecular data. Phylogenetic analyses of the two new families are inferred from the DNA sequences of the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II gene (RPB1), the second largest subunit of RNA polymerase II gene (RPB2), and the translation elongation factor 1-α gene (TEF1). Furthermore, the divergence time of Polyporales was estimated as an additional taxonomic criterion based on the conserved regions of five DNA fragments (5.8S, nLSU, RPB1, RPB2, and TEF1). Bayesian evolutionary analysis revealed that the ancestor of Polyporales splits with a mean stem age of 136.53 Mya with a 95% highest posterior density (HPD) of 118.08-158.06 Mya. The mean stem ages of the families within Polyporales originated between 66.02 and 119.22 Mya, of which Climacocystaceae occurred in a mean stem age of 77.49 Mya with a 95% HPD of 61.45-93.16 Mya, and Gloeoporellaceae occurred in a mean stem age of 88.06 Mya with a 95% HPD of 67.15-107.76 Mya.

Two new species of Hymenochaetaceae from tropical Asia and America

Two new species in Hymenochaetaceae, Fulvifomes acaciae and Pyrrhoderma nigra, are illustrated and described from tropical Asia and America based on morphology and phylogenetic analyses. F. acaciae is characterized by perennial, pileate, and woody hard basidiomata when fresh; ash gray to dark gray, encrusted, concentrically sulcate, and irregularly cracked pileal surface; circular pores of 7-8 per mm with entire dissepiments; a dimitic hyphal system in trama and context; absence of setal element and presence of cystidioles; and broadly ellipsoid, yellowish brown, thick-walled, and smooth basidiospores measuring 5-6 μm × 4-5 μm. P. nigra is characterized by perennial and resupinate basidiomata with dark gray to almost black pore surface when fresh; small and circular pores of 7-9 per mm, a monomitic hyphal system with generative hyphae simple septate, hyphoid setae dominant in subiculum but not in tube trama, and absence of cystidia; and ellipsoid, hyaline, thin-walled basidiospores measuring 4-5 μm × 3-3.6 μm. The differences between the new species and morphologically similar and phylogenetically related species are discussed. Keys to Fulvifomes and Pyrrhoderma have also been provided.

Taxonomy, Phylogeny, Divergence Time Estimation, and Biogeography of the Family Pseudoplagiostomataceae (Ascomycota, Diaporthales)

Species of Pseudoplagiostomataceae were mainly introduced as endophytes, plant pathogens, or saprobes from various hosts. Based on multi-locus phylogenies from the internal transcribed spacers (ITS), the large subunit of nuclear ribosomal RNA gene (LSU), partial DNA-directed RNA polymerase II subunit two gene (rpb2), the partial translation elongation factor 1-alpha gene (tef1α), and the partial beta-tubulin gene (tub2), in conjunction with morphological characteristics, we describe three new species, viz. Pseudoplagiostoma alsophilae sp. nov., P. bambusae sp. nov., and P. machili sp. nov. Molecular clock analyses on the divergence times of Pseudoplagiostomataceae indicated that the conjoint ancestor of Pseudoplagiostomataceae and Apoharknessiaceae occurred in the Cretaceous period. and had a mean stem age of 104.1 Mya (95% HPD of 86.0-129.0 Mya, 1.0 PP), and most species emerged in the Paleogene and Neogene period. Historical biogeography was reconstructed for Pseudoplagiostomataceae by the RASP software with a S-DEC model, and suggested that Asia, specifically Southeast Asia, was probably the ancestral area.

Rapid detection of Heterobasidion annosum using a loop-mediated isothermal amplification assay

Heterobasidion annosum is one of the most aggressive pathogens of Pinus forests in Europe, causing considerable economic losses. To detect H. annosum for disease diagnosis and control, we developed a loop-mediated isothermal amplification (LAMP) reaction with a primer set designed from the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA sequences of H. annosum. In our study, this LAMP assay was found to be capable of efficiently amplifying the target gene within 60 min at 63°C. In specificity tests, H. annosum was positively detected, and other species were negative. The detection limit of this assay was found to be 100 pg·μL^-1, and the assay was also successfully tested for use with basidiospore suspensions and wood samples. This study provides a rapid method for diagnosing root and butt rot caused by H. annosum, which will be of use in port surveillance of logs imported from Europe.

Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis

In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude. By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62-2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene-Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.

Out of the Qinghai-Tibetan plateau: Origin, evolution and historical biogeography of Morchella (both Elata and Esculenta clades)

Introduction

Morchella has become a research hotspot because of its wide distribution, delicious taste, and phenotypic plasticity. The Qinghai-Tibet Plateau subkingdoms (QTPs) are known as the cradle of Ice age biodiversity. However, the diversity of Morchella in the QTPs has been poorly investigated, especially in phylogenetic diversity, origin, and biogeography.

Methods

The genealogical concordance phylogenetic species recognition (GCPSR, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nrLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2)), differentiation time estimation, and ancestral region reconstruction were used to infer Morchella's phylogenetic relationships and historical biogeography in the QTPs.

Results

Firstly, a total of 18 Morchella phylogenetic species are recognized in the QTPs, including 10 Elata clades and 8 Esculenta clades of 216 individuals Secondly, the divergences of the 18 phylogenetic species were 50.24-4.20 Mya (Eocene-Pliocene), which was closely related to the geological activities in the QTPs. Furthermore, the ancestor of Morchella probably originated in the Northern regions (Qilian Shan, Elata cade) and southwestern regions (Shangri-La, Esculenta clade) of QTPs and might have migrated from North America (Rufobrunnea clade) via Beringian Land Bridge (BLB) and Long-Distance Dispersal (LDD) expansions during the Late Cretaceous. Moreover, as the cradle of species origin and diversity, the fungi species in the QTPs have spread out and diffused to Eurasia and South Africa starting in the Paleogene Period.

Conclusion

This is the first report that Esculenta and Elata clade of Morchella originated from the QTPs because of orogenic, and rapid differentiation of fungi is strongly linked to geological uplift movement and refuge in marginal areas of the QTPs. Our findings contribute to increasing the diversity of Morchella and offer more evidence for the origin theory of the QTPs.

Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae)

Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9-81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.

Two new species of Phylloporia (Hymenochaetales) from the Neotropics

Two new species of Phylloporia, P.crystallina and P.sumacoensis, are described based on 28S ribosomal RNA phylogeny, morphology, host, and geographic distribution. Phylloporiacrystallina is characterized by pileate, perennial basidiomata with a duplex context, small pores 9-10 per mm, a monomitic hyphal system, absence of cystidia and cystidioles, presence of large rhomboid crystals in tube trama, broadly ellipsoid to subglobose basidiospores measuring 2.8-3 × 2-2.3 μm, and growth on angiosperm stump. Phylloporiasumacoensis is characterized by pileate, perennial basidiomata with a duplex context, very small pores 10-12 per mm, a monomitic hyphal system, hyphae at dissepiment edges bearing fine crystals, presence of cystidioles, broadly ellipsoid to subglobose basidiospores measuring 3-3.7 × 2.1-2.8 μm, and growth on living liana.

Two new species of Boletopsis (Bankeraceae, Thelephorales) from Southwest China

Two new species of Boletopsis, B.macrocarpa and B.tibetana, are described and illustrated from Southwest (SW) China based on morphology, ecology and phylogenetic analyses by the internal transcribed spacer regions (ITS) and the large subunit of nuclear ribosomal RNA gene (nLSU). Boletopsismacrocarpa is characterized by big basidiocarps (up to 18 cm in diam), guttulate basidiospores, and the presence of gloeoplerous hyphae in context and growing in pure forest of Pinusyunnanensis. Boletopsistibetana is characterized by smaller pores (3-4 per mm), the presence of gloeoplerous hyphae in pileipellis, and the growth in forests of Picea. Phylogenetically, the two new species are grouped in two independent lineages nested in Boletopsis. In addition, one sample from Northeast China is temporarily treated as Boletopsis sp. 1 because of the single sample; another Chinese sample from SW China is sister to B.grisea in phylogeny, and it is treated as B.cf.grisea because the morphological difference between B.cf.grisea and B.grisea is indistinct. Furthermore, the main characteristics of Boletopsis species are listed, and a key to accepted species of Boletopsis is provided.

Taxonomy and an Updated Phylogeny of Anomoloma (Amylocorticiales, Basidiomycota)

Anomoloma is a cosmopolitan poroid wood-decaying genus, belonging to the Amylocorticiales. During a study on polypores, two new species of Anomoloma were found in Eurasia, and they are described as A. denticulatum and A. eurasiaticum. To examine the phylogenetic relationships among species of Anomoloma, we analyzed nuclear ribosomal sequence data from the ITS regions and the LSU gene. The result demonstrates that A. denticulatum and A. eurasiaticum are independent species that belong to the Anomoloma genus. Both new species share the principal characteristics of the genus, but Anomoloma denticulatum is characterized by extensive white rhizomorphs spreading under the whole fruiting body, angular pores measuring 1–2 per mm, distinctly lacerate to dentate dissepiments and basidiospores of 3.5–4.3 × 2–2.5 μm. Anomoloma eurasiaticum is characterized by bearing plenty of large crystals on the mycelia and growth on Picea in high altitude areas. A key to the accepted species of Anomoloma worldwide is provided.

Two New Species of Sidera (Hymenochaetales, Basidiomycota) from Southwest China

Two new wood-inhabiting fungi, Sidera salmonea sp. Nov. and S. tibetica sp. Nov. in the order Hymenochaetales from southwest China, are described and illustrated based on molecular and morphological evidence. They were found on gymnosperm wood that is rotten and charred. The characteristics of S. salmonea include annual, resupinate basidioma, salmon pores with distinctly white margins, angular pores (7–9 per mm), a dimitic hyphal system, and lunate basidiospores that are 3–3.5 × 0.9–1.1 μm. The characteristics of S. tibetica include annual, resupinate basidioma with a white to cream fresh pore surface that becomes cream to honey-yellow and shiny when dry, round pores (7–8 per mm), a dimitic hyphal system, and lunate basidiospores that measure 2.9–3.1 × 1–1.1 μm. A phylogenetic analysis based on the combined 2-locus dataset (5.8S + nuclear large subunit RNA (nLSU)) shows that the two species are members of the genus Sidera, and they are morphologically compared with related species, respectively. This paper provides a key to the identification of 16 accepted species of Sidera that are found throughout the world.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants

Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.

Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies

BACKGROUND

Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies.

RESULTS

We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between plant biotrophic pathogens and other groups (including human, necrotrophic and hemibiotrophic pathogens). The results revealed the biotroph-specific and lifestyle-conserved candidate effector families. These data have been configured in web-based genome browser applications for public display ( http://lab.malab.cn/soft/PFPG ). This resource allows researchers to profile the genome, proteome, secretome and effectome of plant fungal pathogens.

CONCLUSIONS

Our findings demonstrated different genome evolution strategies of plant fungal pathogens with different lifestyles and explored their lifestyle-conserved and specific candidate effectors. It will provide a new basis for discovering the novel effectors and their pathogenic mechanisms.

Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce

Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

Two new species of Hymenochaetaceae on Dracaena cambodiana from tropical China

Two new wood-rotting fungi in the family Hymenochaetaceae, Fulvifomesdracaenicolasp. nov. and Hymenochaetedracaenicolasp. nov., are described and illustrated from tropical China based on morphological characteristics and molecular data. It is worth to mention that both of them grow on Dracaenacambodiana which is a kind of angiosperm tree distributed in tropical regions. F.dracaenicola is characterised by perennial, pileate, triquetrous basidioma with yellowish brown fresh pores which becoming honey yellow with silk sheening upon drying, a dimitic hyphal system in trama and monomitic in context, and subglobose basidiospores measuring 4.8–5 × 4–4.1 μm. H.dracaenicola is characterised by annual, resupinate basidioma with a clay buff hymenophore, a dimitic hyphal system, absence of tomentum and cortex, presence of subulate setae, absence of cystidia, presence of cystidioles and simple hyphidia, and oblong ellipsoid basidiospores measuring 5.2–5.8 × 2.5–2.8 µm. The phylogenetic analyses based on ITS + nLSU rDNA sequences confirm the placement of two new species respectively in Fulvifomes and Hymenochaete. Phylogenetically closely related species to the two new species are discussed.

Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus

Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. vexans, to address the problem of molecular identification within the background of cryptic speciation. The isolation of E. vexans strain was confirmed through morphological studies followed by molecular identification utilizing the developed ITS barcode. Phylogenetic analysis based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) confirmed the molecular identification of the pathogen as E. vexans strain. Further, BI analysis using BEAST mediated the estimation of the divergence time and evolutionary relationship of E. vexans within genus Exobasidium. The speciation process followed the Yule diversification model wherein the genus Exobasidium is approximated to have diverged in the Paleozoic era. The study thus sheds light on the molecular barcode-based species delimitation and evolutionary relationship of E. vexans within its genus Exobasidium.

Taxonomy and Phylogeny of the Fomitopsis pinicola Complex With Descriptions of Six New Species From East Asia

Fomitopsis pinicola is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. In the current study, six new species in the Fomitopsis pinicola complex were discovered from East Asia, based on morphological characters and phylogenetic analyses inferred from the sequence data of the internal transcribed spacer (ITS) regions, the second subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF). Detailed descriptions of the six new species are provided. Our results also indicates that species of the F. pinicola complex from East Asia usually have limited distribution areas and host specialization.

An Updated Global Species Diversity and Phylogeny in the Forest Pathogenic Genus Heterobasidion (Basidiomycota, Russulales)

Heterobasidion species are amongst the most intensively studied polypores because several species are aggressive white rot pathogens of managed coniferous forests mainly in Europe and North America. In the present study, both morphological and multilocus phylogenetic analyses were carried out on Heterobasidion samples from Asia, Oceania, Europe and North America. Three new taxa were found, i.e., H. armandii, H. subinsulare, and H. subparviporum are from Asia and are described as new species. H. ecrustosum is treated as a synonym of H. insulare. So far, six taxa in the H. annosum species complex are recognized. Heterobasidion abietinum, H. annosum, and H. parviporum occur in Europe, H. irregulare, and H. occidentale in North America, and H. subparviporum in East Asia. The North American H. irregulare was introduced to Italy during the Second World War. Species in the H. annosum complex are pathogens of coniferous trees, except H. subparviporum that seems to be a saprotroph. Ten species are found in the H. insulare species complex, all of them are saprotrophs. The pathogenic species are distributed in Europe and North America; the Asian countries should consider the European and North American species as entry plant quarantine fungi. Parallelly, European countries should consider the American H. occidentale and H. irregulare as entry plant quarantine fungi although the latter species is already in Italy, while North America should treat H. abietinum, H. annosum s.s., and H. parviporum as entry plant quarantine fungi. Eight Heterobasidion species found in the Himalayas suggest that the ancestral Heterobasidion species may have occurred in Asia.

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

New Taxon-Specific Heterobasidion PCR Primers Detect and Differentiate North American Heterobasidion spp. in Various Substrates and Led to the Discovery of Heterobasidion irregulare in British Columbia, Canada

Heterobasidion annosum sensu lato is a species complex of pathogenic white-rot wood decay fungi which cause root and butt rot in conifer and hardwood species across the Northern hemisphere. Annual losses to forest managers are valued in the billions of dollars, due to tree mortality, reduction in timber yield, and wood decay. In North America, H. irregulare and H. occidentale have a partially overlapping host and geographic range, cause similar disease symptoms and produce similar fruiting bodies, making discrimination between the two of them often difficult. We developed two sets of primers that bind specifically to conserved, but species-specific portions of glyceraldehyde 3-phosphate dehydrogenase and elongation factor 1α alleles. The method is sensitive enough to detect either species from infected wood. Analysis of North American isolates has further clarified the distribution of both species on this continent, including the detection of H. irregulare for the first time on ponderosa pine (Pinus ponderosa) and eastern white pine (Pinus strobus) in British Columbia. This method has the potential to be a valuable tool for the detection of the pathogen in exported/imported wood products, as well as for the further identification and assessment of the distribution of North American Heterobasidion species.

Crassisporus gen. nov. (Polyporaceae, Basidiomycota) evidenced by morphological characters and phylogenetic analyses with descriptions of four new species

A new poroid wood-inhabiting fungal genus, Crassisporus gen. nov., is proposed on the basis of morphological characters and molecular evidence. The genus is characterized by an annual growth habit, effused-reflexed to pileate basidiocarps with pale yellowish brown to yellowish brown, concentrically zonate or sulcate, and velutinate pileal surface, a trimitic hyphal system with clamped generative hyphae, tissues turning to dark in KOH, oblong to broadly ellipsoid, hyaline, smooth, and slightly thick-walled basidiospores. Phylogenetic analysis based on ITS+nLSU sequences indicate that Crassisporus belongs to the core polyporoid clade. The combined ITS+nLSU+mtSSU+EF1-α+RPB2 sequences dataset of representative taxa in the Polyporaceae demonstrate that Crassisporus is grouped with Haploporus but forms a monophyletic lineage. In addition, four new species of Crassisporus, C. imbricatus, C. leucoporus, C. macroporus, and C. microsporus are described.

Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids

Hybridization may be a major driver in the evolution of plant pathogens. In a high elevation Alpine larch stand in Montana, a novel hybrid fungal pathogen of trees originating from the mating of Heterobasidion irregulare with H. occidentale has been recently discovered. In this study, sequence analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion genotypes collected in the same Alpine larch stand indicated that hybridization has increased allelic diversity by generating novel polymorphisms unreported in either parental species. Sequence data and ploidy analysis through flow cytometry confirmed that heterokaryotic (n + n) genotypes were not first-generation hybrids, but were the result of multiple backcrosses, indicating hybrids are fertile. Additionally, all admixed genotypes possessed the H. occidentale mitochondrion, indicating that the hybrid progeny may have been backcrossing mostly with H. occidentale. Based on reticulate phylogenetic network analysis by PhyloNet, Bayesian assignment, and ordination tests, alleles can be defined as H. irregulare-like or H. occidentale-like. H. irregulare-like alleles are clearly distinct from all known H. irregulare alleles and are derived from the admixing of both Heterobasidion species. Instead, all but one H. occidentale alleles found in hybrids, although novel, were not clearly distinct from alleles found in the parental H. occidentale population. This discovery demonstrates that Alpine larch can be a universal host favouring the interspecific hybridization between H. irregulare and H. occidentale and the hybridization-mediated evolution of a nucleus, derived from H. irregulare parental species but clearly distinct from it.

Species Diversity, Phylogeny, Divergence Time, and Biogeography of the Genus Sanghuangporus (Basidiomycota)

"Sanghuang" is a popular fungus used as a Chinese traditional medicine. In fact, it represents a group of fungi belonging to the genus Sanghuangporus, but little is known about its origin and biogeography. The aim of this study was to characterize the molecular relationships, origin and biogeographical distribution of Sanghuangporus. The multi-locus phylogenetic analyses were used to infer the phylogenetic relationships. In addition, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), we used a fungus fossil-based approach to gain insight into the divergence time of species in Sanghuangporus. The molecular phylogeny strongly supports the monophyly of Sanghuangporus (MP = 100%, ML = 100%, and BPP = 1.00), and 13 species are recognized in this genus. The Bayesian uncorrelated lognormal relaxed molecular clock using BEAST and reconstructed ancestral areas indicate that the maximum crown age of Sanghuangporus is approximately 30.85 million years. East Asia is the likely ancestral area (38%). Dispersal and differentiation to other continents then occurred during the late Middle Miocene and Pliocene. The ancestor of Sanghuangporus probably originated in palaeotropical Northeast Asia and covered Northeast Asia and East Africa during the Oligocene-Miocene, hosted by plants that expanded via the "Gomphotherium Landbridge." Six kinds of dispersal routes are proposed, including intercontinental dispersal events of three clades between Northeast Asia and East Africa, between East Asia and North America, and between Northeast Asia and Europe.

Cryptic Speciation in Western North America and Eastern Eurasia of the Pathogens Responsible for Laminated Root Rot

Coniferiporia sulphurascens is a facultative fungal pathogen that causes laminated root rot (LRR) in commercially important coniferous species worldwide. This fungus spreads primarily by way of vegetative mycelium transferring at points of contact between infected and healthy roots. Successful intervention to control LRR requires a better understanding of the population structure and genetic variability of C. sulphurascens. In this study, we investigated the population genetic structure and origin of C. sulphurascens populations in western North America and eastern Eurasia collected from multiple coniferous hosts. By analyzing the small and large mitochondrial ribosomal RNA subunit genes combined with six nuclear loci (internal transcribed spacer region, actin, RNA polymerase II largest subunit, RNA polymerase II second-largest subunit, laccase-like multicopper oxidase, and translation elongation factor 1-α), we observed that none of the alleles among the loci were shared between North American (NA) and Eurasian C. sulphurascens populations. In total, 55 multilocus genotypes (MLGs) were retrieved in C. sulphurascens isolates occurring in these two continental regions. Of these, 41 MLGs were observed among 58 isolates collected from widespread locations in British Columbia (Canada) and the northwestern United States, while 14 MLGs were observed among 16 isolates sampled in Siberia and Japan. Our data showed that the levels of genetic differentiation between the NA and Eurasian populations are much greater than the populations from within each continental region; the two continental populations formed clearly divergent phylogenetic clades or lineages since they were separated approximately 7.5 million years ago. Moreover, the Eurasian population could be the source of the NA population. Our study indicates the existence of cryptic diversity in this pathogen species, and strongly suggests that the NA and Eurasian populations represent two lineages, which have progressively diverged from each other in allopatry.

The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa (Crustacea: Decapoda: Parathelphusidae)

In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab. The authors established the phylogenetic relationships using the maximum likelihood and Bayesian inference methods. The phylogenetic relationship indicated that the molecular taxonomy of S. boyangensis is consistent with current morphological classification, and Parathelphusidae and Potamidae are derived within the freshwater clade or as part of it. In addition, the authors used the COX1 sequence of Somanniathelphusa in GenBank and the COX1 sequence of S. boyangensis to estimated the divergence time of this genus. The result displayed that the divergence time of Somanniathelphusa qiongshanensis is consistent with the separation of Hainan Island from mainland China in the Beibu Gulf, and the divergence time for Somanniathelphusa taiwanensis and Somanniathelphusa amoyensis is consistent with the separation of Taiwan Province from Mainland China at Fujian Province. These data indicate that geologic events influenced speciation of the genus Somanniathelphusa.

Heterobasidion Partitivirus 13 Mediates Severe Growth Debilitation and Major Alterations in the Gene Expression of a Fungal Forest Pathogen

The fungal genus Heterobasidion includes some of the most devastating conifer pathogens in the boreal forest region. In this study, we showed that the alphapartitivirus Heterobasidion partitivirus 13 from Heterobasidion annosum (HetPV13-an1) is the main causal agent of severe phenotypic debilitation in the host fungus. Based on RNA sequencing using isogenic virus-infected and cured fungal strains, HetPV13-an1 affected the transcription of 683 genes, of which 60% were downregulated and 40% upregulated. Alterations observed in carbohydrate and amino acid metabolism suggest that the virus causes a state of starvation, which is compensated for by alternative synthesis routes. We used dual cultures to transmit HetPV13-an1 into new strains of H. annosum and Heterobasidion parviporum The three strains of H. parviporum that acquired the virus showed noticeable growth reduction on rich culturing medium, while only two of six H. annosum isolates tested showed significant debilitation. Based on reverse transcription-quantitative PCR (RT-qPCR) analysis, the response toward HetPV13-an1 infection was somewhat different in H. annosum and H. parviporum We assessed the effects of HetPV13-an1 on the wood colonization efficacy of H. parviporum in a field experiment where 46 Norway spruce trees were inoculated with isogenic strains with or without the virus. The virus-infected H. parviporum strain showed considerably less growth within living trees than the isolate without HetPV13-an1, indicating that the virus also causes growth debilitation in natural substrates.IMPORTANCE A biocontrol method restricting the spread of Heterobasidion species would be highly beneficial to forestry, as these fungi are difficult to eradicate from diseased forest stands and cause approximate annual losses of €800 million in Europe. We used virus curing and reintroduction experiments and RNA sequencing to show that the alphapartitivirus HetPV13-an1 affects many basic cellular functions of the white rot wood decay fungus Heterobasidion annosum, which results in aberrant hyphal morphology and a low growth rate. Dual fungal cultures were used to introduce HetPV13-an1 into a new host species, Heterobasidion parviporum, and field experiments confirmed the capability of the virus to reduce the growth of H. parviporum in living spruce wood. Taken together, our results suggest that HetPV13-an1 shows potential for the development of a future biocontrol agent against Heterobasidion fungi.

Fungi and fungal interactions in the Rhynie chert: a review of the evidence, with the description of Perexiflasca tayloriana gen. et sp. nov.†

The Lower Devonian Rhynie chert is one of the most important rock deposits yielding comprehensive information on early continental plant, animal and microbial life. Fungi are especially abundant among the microbial remains, and include representatives of all major fungal lineages except Basidiomycota. This paper surveys the evidence assembled to date of fungal hyphae, mycelial cords and reproductive units (e.g. spores, sporangia, sporocarps), and presents examples of fungal associations and interactions with land plants, other fungi, algae, cyanobacteria and animals from the Rhynie chert. Moreover, a small, chytrid-like organism that occurs singly, in chain-like, linear arrangements, planar assemblages and three-dimensional aggregates of less than 10 to [Formula: see text] individuals in degrading land plant tissue in the Rhynie chert is formally described, and the name Perexiflasca tayloriana proposed for the organism. Perexiflasca tayloriana probably colonized senescent or atrophied plant parts and participated in the process of biological degradation. The fungal fossils described to date from the Rhynie chert constitute the largest body of structurally preserved evidence of fungi and fungal interactions from any rock deposit, and strongly suggest that fungi played important roles in the functioning of the Early Devonian Rhynie ecosystem.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Phylogeny and diversity of the morphologically similar polypore genera Rigidoporus, Physisporinus, Oxyporus, and Leucophellinus

Rigidoporus and its morphologically similar genera Physisporinus, Oxyporus, and Leucophellinus, which include some forest pathogens and medicinal species, are very important groups of wood-decaying fungi. Species of these genera have not only ecological functions, but also economic importance. Phylogenetic and taxonomic studies on taxa in these genera were carried out. Inferred from phylogenies based on DNA sequences of the nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) and D1-D2 domains of nuc 28S rDNA, 36 species sampled that traditionally belong to Physisporinus, Rigidoporus, Leucophellinus, and Oxyporus are nested mostly in eight lineages. Of these lineages, five (including four genera of Physisporinus, Emmia, Flaviporus, and Flavodon and one taxon "R. hypobrunneus") belong to Polyporales and three (including the genera Rigidoporus, Bridgeoporus, and Leucophellinus) belong to Hymenochaetales. Rigidoporus and Oxyporus are merged because the type species of both genera are nested in a single lineage within Hymenochaetales. Some taxon previously placed in Ceriporia and Oxyporus are transferred to Emmia and Flavodon, respectively, on the basis of current phylogeny. Utilizing a combination of the morphological and phylogenetic evidence, 16 new combinations in Bridgeoporus, Emmia, Flaviporus, Flavodon, Rigidoporus, and Physisporinus are proposed. Five new species, Physisporinus crataegi, P. lavendulus, P. subcrocatus, P. tibeticus, and Rigidoporus submicroporus, are recognized from China. Illustrated descriptions of these novel species are provided. Three taxa are treated at the generic level of Physisporinus because of limited samples.

Phylogeny and taxonomy of Favolus (Basidiomycota)

Favolus is a natural genus that is closely related to Polyporus. A taxonomic study of Favolus was carried out based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2 = ITS) and 18S and 28S genes of the nuc rDNA, translation elongation factor 1-α gene (TEF1-α), the mt 16S rDNA gene (mt rrnS), β-tubulin gene (TBB1), and the RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2) genes. Fourteen specimens collected from subtropical to tropical regions in China were shown to be different from existing Favolus species. They are described and illustrated here as four new species, namely, Favolus niveus, F. septatus, F. pseudoemerici, and F. subtropicus.

Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau

Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.

Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales)

BACKGROUND

The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU).

RESULTS

Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area.

CONCLUSIONS

Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

Global diversity and phylogeny of Onnia (Hymenochaetaceae) species on gymnosperms

Onnia includes white rotting polypores with annual basidiocarps, a duplex context, monomitic hyphal structure, hymenial setae, and hyaline, thin-walled, smooth basidiospores. Specimens of Onnia, originating mainly from East Asia, Europe, and North America, were studied using both morphology and phylogenetic analyses. Our concatenated data set was derived from 25 collections and included (i) 25 nuc rDNA internal transcribed spacer region sequences (ITS1-5.8S-ITS2 = ITS), 17 generated in this study; and (ii) 14 nuc rDNA 28S rDNA sequences, including the D1-D2 domains, 11 of them generated in this study. The resulting maximum likelihood and Bayesian phylogenies recovered all sampled collections of Onnia as a well-supported clade. In this clade, three previously accepted species, viz., Onnia leporina, O. tomentosa, and O. triquetra, received strong support, whereas three additional lineages with strong support represent the new species described in this paper, O. subtriquetra, O. microspora, and O. tibetica. Of the six Onnia species occurring on gymnosperms, O. tomentosa and O. leporina grow mainly on Picea and have circumboreal distribution in the Northern Hemisphere. In contrast, other species that mostly grow on Pinus are geographically restricted to limited regions, viz., O. triquetra in Europe, O. subtriquetra in North America, and O. microspora and O. tibetica in Asia.

Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales)

Bondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). From the results, we inferred that the maximum crown age of Bondarzewia is approximately 25.5 million-years-ago (Mya) and that tropical East Asia is likely to be its ancestral area, with three possible expansions leading to its distribution in North America, Europe and Oceania.

Taxonomy and Phylogeny of Polyporus Group Melanopus (Polyporales, Basidiomycota) from China

Melanopus is a morphological group of Polyporus which contains species with a black cuticle on the stipe. In this article, taxonomic and phylogenetic studies on Melanopus group were carried out on the basis of morphological characters and phylogenetic evidence of DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit nuclear ribosomal RNA gene (nSSU), the small subunit mitochondrial rRNA gene sequences (mtSSU), the translation elongation factor 1-α gene (EF1-α), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II (RPB2), and β-tubulin gene sequences (β-tubulin). The phylogenetic result confirmed that the previously so-called Melanopus group is not a monophyletic assemblage, and species in this group distribute into two distinct clades: the Picipes clade and the Squamosus clade. Four new species of Picipes are described, and nine new combinations are proposed. A key to species of Picipes is provided.

Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.)

Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before.