Fungal Planet description sheets: 1112-1181

Abstract

Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.

Keywords: ITS nrDNA barcodes; LSU; new taxa; systematics.

Overview Agaricomycetes phylogeny – part 1

Consensus phylogram (50 % majority rule) of 435 752 trees resulting from a Bayesian analysis of the LSU sequence alignment (130 sequences including outgroup; 979 aligned positions; 571 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Backusella lamprospora (GenBank MH866118.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Agaricomycetes phylogeny – part 1

Consensus phylogram (50 % majority rule) of 435 752 trees resulting from a Bayesian analysis of the LSU sequence alignment (130 sequences including outgroup; 979 aligned positions; 571 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Backusella lamprospora (GenBank MH866118.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Dothideomycetes phylogeny – part 1

Consensus phylogram (50 % majority rule) of 146 328 trees resulting from a Bayesian analysis of the LSU sequence alignment (233 sequences including outgroup; 824 aligned positions; 341 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Diaporthe perjuncta (GenBank NG_059064.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Dothideomycetes phylogeny – part 1

Consensus phylogram (50 % majority rule) of 146 328 trees resulting from a Bayesian analysis of the LSU sequence alignment (233 sequences including outgroup; 824 aligned positions; 341 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Diaporthe perjuncta (GenBank NG_059064.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Dothideomycetes phylogeny – part 1

Consensus phylogram (50 % majority rule) of 146 328 trees resulting from a Bayesian analysis of the LSU sequence alignment (233 sequences including outgroup; 824 aligned positions; 341 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Diaporthe perjuncta (GenBank NG_059064.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Eurotiomycetes phylogeny

Consensus phylogram (50 % majority rule) of 146 252 trees resulting from a Bayesian analysis of the LSU sequence alignment (70 sequences including outgroup; 838 aligned positions; 267 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Diaporthe perjuncta (GenBank NG_059064.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Geoglossomycetes phylogeny

Consensus phylogram (50 % majority rule) of 46 502 trees resulting from a Bayesian analysis of the LSU sequence alignment (18 sequences including outgroup; 930 aligned positions; 223 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. The family and order are indicated with coloured blocks to the right of the tree. GenBank accession or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Aspergillus niger (GenBank KC119204.1) and the taxonomic novelty described in this study for which LSU sequence data were available is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Leotiomycetes phylogeny

Consensus phylogram (50 % majority rule) of 222 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (78 sequences including outgroup; 839 aligned positions; 258 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. Family assignment for Helotiales follows Johnston et al. (2019). GenBank accession or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Xylaria hypoxylon (GenBank AY544648.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Pezizomycetes phylogeny

Consensus phylogram (50 % majority rule) of 52 502 trees resulting from a Bayesian analysis of the LSU sequence alignment (31 sequences including outgroup; 821 aligned positions; 204 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. The family and order are indicated with coloured blocks to the right of the tree. GenBank accession or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Candida broadrunensis (GenBank KY106372.1) and the taxonomic novelty described in this study for which LSU sequence data were available is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Phytophthora phylogeny

Consensus phylogram (50 % majority rule) of 1 260 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (51 sequences including outgroup; 1 305 aligned positions; 130 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. The family and order are indicated with coloured blocks to the right of the tree. GenBank accession or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Absidia panacisoli (GenBank NG_063948.1) and the taxonomic novelty described in this study for which LSU sequence data were available is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Saccharomycetes phylogeny

Consensus phylogram (50 % majority rule) of 69 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (33 sequences including outgroup; 553 aligned positions; 198 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. The families and order are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Backusella lamprospora (GenBank MH866118.1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Sordariomycetes ( Hypocreales ) phylogeny – part 1

Consensus phylogram (50 % majority rule) of 1 695 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (135 sequences including outgroup; 812 aligned positions; 341 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and the order are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Ramularia endophylla (GenBank AY490776.2) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Sordariomycetes ( Hypocreales ) phylogeny – part 1

Consensus phylogram (50 % majority rule) of 1 695 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (135 sequences including outgroup; 812 aligned positions; 341 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and the order are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Ramularia endophylla (GenBank AY490776.2) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Sordariomycetes (Other orders) phylogeny

Consensus phylogram (50 % majority rule) of 60 752 trees resulting from a Bayesian analysis of the LSU sequence alignment (41 sequences including outgroup; 807 aligned positions; 247 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Ramularia endophylla (GenBank AY490776.2) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Overview Sordariomycetes ( Xylariales ) phylogeny

Consensus phylogram (50 % majority rule) of 528 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (49 sequences including outgroup; 815 aligned positions; 218 unique site patterns) using MrBayes v. 3.2.7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0.84 are shown at the nodes and thickened lines represent nodes with PP = 1.00. The scale bar represents the expected changes per site. Families and the order are indicated with coloured blocks to the right of the tree. GenBank accession and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Ramularia endophylla (GenBank AY490776.2) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 27179).

Neocalonectria tristaniopsidis

Gobabebomyces vachelliae

Graminopassalora geissorhizae

Juncomyces patwiniorum

Davidhawksworthia quintiniae

Cylindromonium alloxyli

Parasarocladium tasmanniae

Exophiala mali

Linteromyces quintiniae

Xyladictyochaeta tristaniopsidis

Exophiala prostantherae

Talaromyces pulveris

Neocamarosporium leipoldtiae

Dothiora aloidendri & Hantamomyces aloidendri

Suttonomyces cephalophylli

Endoconidioma euphorbiae

Neometulocladosporiella seifertii

Verrucocladosporium carpobroti

Stemphylium carpobroti

Neocladosporium osteospermi

Eucasphaeria proteae

Paramyrothecium pituitipietianum

Polyscytalum pini-canariensis

Acremonium behniae

Alternaria mirabibensis

Preussia procaviae

Curvularia moringae & Moringomyces phantasmae

Neodothiora populina

Amanita domingensis

Austroboletus asper

One of 119 equally most parsimonious trees based on sequences of nrITS, nrLSU, and tef1, with node support above branches from Bayesian inference (BI: MrBayes v. 3.2.6, Ronquist et al. 2012), 1 000 bootstrap replicates in maximum likelihood (ML; MEGA X, Kumar et al. 2018, Stecher et al. 2020), and 100 bootstrap replicates in maximum parsimony (MP; PAUP v. 4.0b10, Swofford 2003), and percent consensus among the 119 equally most parsimonious MP trees below. Branches with less than 50 % support are marked with dashes (--) and those that collapsed in a particular analysis are marked with asterisks (**). New sequences are indicated in bold, and sequences from types are indicated as HT (holotype) or NT (neotype).

Cantharellus betularum

Chaetothyrina spondiadis

Maximum Likelihood tree obtained from ITS sequences of our isolate and sequences retrieved from the GenBank nucleotide database. The tree was built by using PhyML v. 3.0 (Guindon et al. 2010a, b). Bootstrap support values (≥ 70 %) are given above the branches. Mucor simplex CBS 428.80 was used as outgroup. The new species proposed in the present study is indicated in bold. ^T = ex-type.

Circinella lampensis

Phylogenetic tree from Bayesian analysis based on combined gene sequences (chs-1, gapdh, ITS and tub2) showing the phylogenetic relationships amongst the newly described taxon C. cycadis (in bold) and known species in the C. gloeosporoides complex. Bayesian posterior probabilities (PP > 0.95) are shown at the nodes. The tree is rooted with C. boninense (ICMP 17904). Ex-type cultures are marked with an asterisk (*). The alignment and tree were deposited in TreeBASE (Submission ID S26714).

Colletotrichum cycadis

Phylogram obtained using PAUP* v. 4.0a (Swofford 2003) based on ITS and LSU sequence data showing the position of C. rubra in the Atramentarii and Lanatuli clades (Nagy et al. 2013). Bootstrap values are indicated on branches and the holotype is marked in bold.

Coprinopsis rubra

Crinipellis nigrolamellata

Maximum likelihood (ML) tree for the Cyberlindnera clade obtained from the combined analysis of ITS and LSU sequence data. The alignment included 1 194 bp and was performed with MAFFT v. 7 (Katoh et al. 2019). The General Time Reversible model (GTR) with Gamma distribution and invariant sites (G+I) was used as the best nucleotide substitution model. The phylogenetic analysis was conducted in MEGA v. 6 (Tamura et al. 2013). Pichia membranifaciens NRRL Y-2026 (DQ104710/U75725) was used as outgroup (hidden).

Cyberlindnera dauci

Cyphellophora vietnamensis

Elaphomyces nemoreus

Maximum likelihood tree (RAxML, conducted in the CIPRES science gateway) from the analysis of combined ITS, LSU, tef1 and tub2 sequences (total 1 957 bp) of members of the Exophiala salmonis clade. Bootstrap support values above 70 % are indicated on the nodes. The new species proposed in this study is indicated in bold. T and IT denotes ex-type and ex-isotype cultures. GenBank reference sequence accession numbers for ITS, LSU, tef1 and tub2 are indicated between parentheses. The tree is rooted to Cladophialophora modesta (CBS 985.96).

Exophiala embothrii

The Bayesian majority-rule consensus tree was inferred from the concatenated dataset of ITS-LSU sequences. The dataset included G. jirinae (H: holotype), relevant Geoglossum species, and Leucoglossum leucosporum as an outgroup (TreeBASE study S26857). Bayesian inference was run in MrBayes v. 3.2.7a, using four independent chains, 10 M generations, and a sampling frequency of 1 000 (Ronquist et al. 2012). The best-fit partitioning schemes and models were estimated for the concatenated tree, using the greedy search mode as implemented in the PartitionFinder v. 2.1.1 (Lanfear et al. 2016). The maximum likelihood analysis was computed in RAxML v. 8.2.12 (Stamatakis 2014). Analyses were computed in the CIPRES Science Gateway v. 3.3 (Miller et al. 2010). Numbers above branches indicate Bayesian posterior probabilities ≥ 0.95 and the maximum likelihood bootstrap support values ≥ 85 %. The scale bar represents the number of nucleotide changes per site.

Geoglossum jirinae

Phylogenetic placement of Gymnascella minnisii compared to close relatives on a maximum likelihood tree with maximum likelihood/maximum parsimony bootstrap support values. Gymnascella minnisii is highlighted in bold. This analysis was based on a single gene alignment, utilising nrDNA sequences (ITS1, ITS4 primers; White et al. 1990) only. PAUP v. 4.0a build 167 (Swofford 2003) was utilised to conduct the 1 000 bootstrap maximum parsimony analysis and maximum likelihood analysis. The maximum likelihood analysis utilised the General Time Reversible (GTR) nucleotide model with rate matrix set to estimate, and variable sites set to gamma distribution. Bootstrap support values greater than 70 % are shown on nodes in the following order: maximum likelihood/maximum parsimony. The alignment was deposited in TreeBASE (submission S26902).

Gymnascella minnisii

Pseudogymnoascus palmeri

Maximum likelihood tree of LSU sequences generated using RAxML HPC2 (Stamatakis 2014) on the CIPRES v. 3.3 portal (Miller et al. 2010). Hypoxylon hepaticolor is in bold. RAxML bootstrap support values above 70 % are shown above the nodes and Bayesian posterior probability scores above 0.95 are shown as thickened branches. GenBank accession numbers for LSU sequences are given after taxon names.

Hypoxylon hepaticolor

Phylogram based on ITS and LSU sequence data showing the position of I. iololepis in the I. lilacina group. Bootstrap support values are indicated on branches and the sequence of the holotype is marked in bold. Multiple sequence alignments were carried out with MAFFT (https://mafft.cbrc.jp/alignment/server/). The alignment was checked and adjusted manually, heuristic searches and bootstrap parsimony analyses were performed using PAUP v. 4.0b10 (Swofford 2003).

Inocybe ionolepis

Lactifluus lactiglaucus

Mid-point rooted phylogram from a maximum likelihood search using IQ-TREE v. 1.3.11.1 (Nguyen et al. 2015) with 10 000 ultra-fast bootstraps (Minh et al. 2013), 10 000 replicates of an approximate likelihood ratio test (aLRT), and a best-fit model of evolution (command -m TEST). ITS sequences aligned with MAFFT in UGENE v. 1.30.0 (Okonechnikov et al. 2012). The aLRT and UFBootstrap values are indicated at nodes. Minimum spanning network of all available Lophotrichus ITS sequences generated using POPART v. 1.7 (Leigh & Bryant 2015); hashes indicate number of parsimony informative characters between taxa.

Lophotrichus medusoides

Maximum-likelihood analysis of the nrITS region of Melanoleuca subg. Urticocystis species was performed with RAxML v. 8 (Stamatakis 2014) using the GTR+G model (1 000 bootstrap replicates). Only maximum-likelihood bootstrap support values ≥ 70 % are shown in the phylogenetic tree. The scale bar represents the number of nucleotide changes per site.

Melanoleuca dominicana

Moelleriella puertoricoensis

Maximum likelihood tree of the ITS-nrDNA for a selection of Mycena species, aligned using MUSCLE and constructed using MEGA X.

Mycena pulchra

Maximum likelihood tree of Penicillium strains belonging to section Exilicaulis series Erubescentia based on 1 871 aligned nucleotides (combined BenA, CaM and RPB2 sequences). Strain and GenBank accession numbers used in the analysis can be found in Houbraken et al. (2020). Analysis performed using RAxML v. 8.2.12 (Stamatakis 2014). Bootstrap 1 000 re-samplings; only bootstrap support values above 70 % are presented at the nodes and branches of > 95 % are thickened. Penicillium fractum and P. inusitatum were used as outgroup. The scale bar indicates the number of substitutions per site.

Penicillium vallebormidaense

Penicillium saanichanum

Phialocephala melitaea

Bayesian inference tree based on a concatenated ITS, Btub, hsp90, coxI and nadh1 sequence alignment showing the placement of Phytophthora aquae-cooljarloo in Phytophthora Clade 6a. The tree was generated in MrBayes v. 3.2.6 (Huelsenbeck & Ronquist 2001) as a plugin in Geneious Prime→ 2019.2.3 (www.geneious.com) using the GTR substitution model. The posterior probability values are shown at the nodes. The tree was rooted to P. thermophila (not shown) and the novel species is shown in bold font.

Phytophthora aquae-cooljarloo

Phytopythium paucipapillatum

Maximum Likelihood tree inferred with MEGA v. 6 software (Tamura et al. 2013) from the combined CAL, ITS and RPB1 gene regions of 39 isolates. The novel species is shown in bold. Bootstrap support values from ML ≥ 90 % are provided above internodes.

Pseudopyricularia javanii

Phylogenetic tree based on Maximum likelihood analysis obtained by RAxML using the combined LSU and ITS sequences of Pseudosubramaniomyces and related genera in the family Beltraniaceae. Bootstrap support values above 70 % are indicated on the nodes. The alignment included 1 530 bp and was performed using Kimura-2 parameter Gamma distribution with Invariant sites (G+I) as the best nucleotide substitution model. The tree was rooted with Seimatosporium elegans NBRC 32674 and Seimatosporium eucalypti CPC 159. The alignment was constructed with MEGA v. 6 software (Tamura et al. 2013). The new species proposed in this study is indicated in bold face. A superscript ^T denotes ex-type cultures.

Pseudosubramaniomyces septatus

Maximum likelihood tree obtained from the ITS, tub2, LSU and rpb2 gene sequences of Pyrenochaetopsis species of our isolates and sequences retrieved from GenBank. The tree was built using MEGA v. 7.0 (Kumar et al. 2016). The combined LSU, ITS, tub2 and rpb2 sequence data set consisted of 17 Pyrenochaetopsis strains with Xenopyrenochaetopsis pratorum and Neopyrenochaetopsis hominis as the outgroup taxa and consisted of 2 195 characters. Of these 1 643 were constant, 188 were variable and parsimony-uninformative and 337 were parsimony-informative. A heuristic search of these 337 parsimony-informative characters resulted in 1 000 equally parsimonious trees of 467 steps with CI = 0.72, RI = 0.65 and HI = 0.28. The ML analysis yielded a best scoring tree with the final ML optimization likelihood value of –4554.41 (ln) and a gamma distribution shape parameter value of α = 0.1411. All individual trees obtained from single gene datasets were essentially similar in topology and not substantially different from the tree generated from the concatenated dataset. One of the two ML trees obtained is presented with ML/MP bootstrap support values at the nodes. The alignment and tree are available in TreeBASE (Submission ID: 26835).

Pyrenochaetopsis rajhradensis

Russula shawarensis

Bayesian inference tree of ITS sequences from S. whamiae (bold) and related Sebacinales species in GenBank using MrBayes v. 3.2.7 (Huelsenbeck & Ronquist 2001) as implemented in Geneious v. 10.2.6 (Kearse et al. 2012). ClustalW was used for the alignment. The numbers above the branches are Bayesian posterior probabilities with values less than 0.7 not shown. Helvellosebacina sp. (KF000449) and Sebacina incrustans (JQ66545) were used as outgroups. Sequences labelled OTUA etc. are Australian orchid isolates categorised by Whitehead et al. (2017). Sequences in red are named species of Serendipita.

Serendipita whamiae

Phylogenetic tree obtained by the analysis of combined ITS and LSU nrDNA sequences of Suhomyces rilaensis DZ3^T and related species using a neighbour-joining method (Kimura two-parameter model; MEGA v. 7; 100 bootstrap replicates).

Suhomyces rilaensis

Phylogenetic tree with T. flavonigrum constructed from a combined dataset comprising LSU, tef1 and rpb1. The phylogenetic tree was analysed using Maximum parsimony (MP), Maximum likelihood (ML) and Bayesian inference. The MP analysis was conducted on the combined data set using PAUP v. 4.0b10 (Swofford 2003), adopting random addition sequences (100 replications), with gaps being treated as missing data. A bootstrap (BP) analysis was performed using the maximum parsimony criterion in 1 000 replications. The ML analysis was run with RAxML-VI-HPC2 v. 8.2.12 (Stamatakis 2014) under a GTR model, with 1 000 bootstrap replicates. Bayesian phylogenetic inference was calculated with MrBayes v. 3.2.6 (Ronquist & Huelsenbeck 2003), with 5 M generations and under the same model. Numbers at the significant nodes represent MP bootstrap support values/RAxML bootstrap support values/Bayesian posterior probabilities (BPP) times 100. Thickened lines in the tree represent 99–100 % bootstrap support values and 99–100 BPP.

Tolypocladium flavonigrum

Maximum likelihood (ML) phylogenetic tree inferred from ITS sequences using RAxML-HPC v. 8 (Stamatakis 2014) on XSEDE in the CIPRES science gateway (Miller et al. 2010). GTR + G was selected as model of evolution for the analysis. The sequences obtained in the present study are highlighted in bold. Bootstrap support values (≥ 70 %) are indicated at the nodes. Tuber latisporum and Tuber pseudosphaerosporum were used as outgroup. The scale bar indicates the expected changes per site.

Tuber lusitanicum

Tylopilus subotsuensis

Veloboletus limbatus

Xenomonodictys iranica

Cortinarius indopurpurascens

Cortinarius glaucoelotus