The Molecular Systematics of Unitunicate, Perithecial Ascomycetes.

Maximum parsimony analysis of partial sequences from the small subunit ribosomal DNA (ssrDNA) rejects the monophyly of unitunicate, perithecial ascomycetes (pyrenomycetes). The genera Kathistes, Pyxidiophora and Subbaromyces are separated from a large clade of relatively derived pyrenomycetes. This derived pyrenomycete clade is supported by a bootstrap confidence level of 100% and a decay index of $\u3e$10 steps, and contains two subclades, A and B. Subclade A comprises the orders Clavicipitales, Hypocreales, Microascales and the genus Ceratocystis; subclade B consists of the Diaporthales, Sordariales, Xylariales and the genus Ophiostoma. The Clavicipitales is a sister taxon to the Hypocreales, which consists of two paraphyletic lineages. The ophiostomatalean taxa sampled do not form a monophyletic group; the data support the removal of Ophiostoma H. & P. Sydow from Ceratocystis Ellis and Halst. as proposed by several investigators. The Xylaria and Ophiostoma centrum types of Luttrell (1951) are inconsistent with the monophyletic groups inferred from the ssrDNA. Hypotheses concerning the evolution of centrum development are refined in light of these data. An additional data set was derived from the B subunit of vacuolar ATPase (BvATPase) to provide an independent test of the ssrDNA gene tree and morphologically based hypotheses. Analysis of the first and second position of the codon support the separation of the genera Pyxidiophora and Subbaromyces from the larger clade of relatively derived pyrenomycetes. Inclusion of the third position of the codon does not support the separation of these genera from the larger clade of relatively derived pyrenomycetes or relationships within the derived clade that are mutually supported by the ssrDNA and morphology. Over 95% of the third codon positions sampled were variable, which constituted 76% of the synapomorphies of the BvATPase data set. Retention indices (RI) and rescaled consistency indices (RC) of the two BvATPase data sets suggest that the third codon position is too variable with respect to frequency of characters state variation and distribution of character states for use in the systematics of the taxa sampled. The nonmonophyly of unitunicate, perithecial ascomycetes is suggested to be the better of two hypotheses

The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

Abstract Background Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens. Results The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation. Conclusions Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.http://deepblue.lib.umich.edu/bitstream/2027.42/112062/1/12864_2015_Article_1777.pd

Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus . Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont

Rhizopogon togasawariana sp. nov., the first report of Rhizopogon associated with an Asian species of Pseudotsuga

Rhizopogon subgenus Villosuli are the only members of the genus known to form an ectomycorrhizal relationship exclusively with Pseudotsuga. The specificity of this host relationship is unusual in that Rhizopogon is broadly associated with several tree genera within the Pinaceae and relationships with a host genus are typically distributed across Rhizopogon subgenera. Naturally occurring specimens of R. subg. Villosuli have been described only from North American collections, and the unique host relationship with Pseudotsuga is demonstrated only for Rhizopogon associated with P. menziesii (Douglas-fir), the dominant species of Pseudotsuga in North America. Species of Pseudotsuga are naturally distributed around the northern Pacific Rim, and Rhizopogon associates of other Pseudotsuga spp. are not yet described. Here we present the results of field sampling conducted in P. japonica forests throughout the Japanese archipelago and describe Rhizopogon togasawariana sp. nov., which occurs in ectomycorrhizal association with P. japonica. Placement of this new species within R. subg. Villosuli is supported by morphological and molecular phylogenetic analysis, and its implications to Pseudotsuga-Rhizopogon biogeography are discussed.This is the publisher’s final pdf. The article is copyrighted by the Mycological Society of America and published by Allen Press Inc. It can be found at: http://www.mycologia.org/.Keywords: Truffle, Japan, Rhizopogon subgenus Villosuli, Biogeography, Ectomycorrhizae, Hypogeou

The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

Background Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens. Results The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation. Conclusions Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.Keywords: Lineage sorting, Mycoparasites, Hypocreales, Secondary metabolis

Morphological and genetic characterisation of Beauveria sinensis sp. nov. from China

Beauveria sinensis sp. nov. was isolated from a larva of Geometridae (Lepidoptera) collected from Tiantangzhai, Anhui province, China. It is characterized by elongated ellipsoidal to cylindrical conidia, solitary conidiogenous cells that are cylindrical or with slightly swollen bases, white to pale pink colony in culture, and small mycelial pellets consisting of curved hyphae. Phylogenetic analyses of translation elongation factor-1 alpha (TEF), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) sequence data support it as a unique species and sister to B. sungii. It does not, however, form a monophyletic group with other elongated ellipsoidal to cylindrical conidia-producing species in Beauveria. Type isolates and holotype are deposited in the Research Center for Entomogenous Fungi of Anhui Agricultural University (RCEF).Keywords: taxonomy, entomopathogenic fungi, Ascomycete

The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often found to reflect the structure of phylogenies based on molecular data, many species remain of uncertain placement due to a lack of reliable data or conflicting morphological characters. A rigid, darkly pigmented stipe and the production of a Hirsutella-like anamorph in culture were taken as evidence for the transfer of the species Cordyceps cuboidea, Cordyceps prolifica, and Cordyceps ryogamiensis to the genus Ophiocordyceps. Data from ribosomal DNA supported these species as a single group, but were unable to infer deeper relationships in Hypocreales. Here, molecular data for ribosomal and protein coding DNA from specimens of Ophiocordyceps cuboidea, Ophiocordyceps ryogamiensis, Ophiocordyceps paracuboidea, Ophiocordyceps prolifica, Cordyceps ramosopulvinata, Cordyceps nipponica, and isolates of Polycephalomyces were combined with a broadly sampled dataset of Hypocreales. Phylogenetic analyses of these data revealed that these species represent a clade distinct from the other clavicipitoid genera. Applying the recently adopted single system of nomenclature, new taxonomic combinations are proposed for these species in the genus Polycephalomyces, which has been historically reserved for asexual or anamorphic taxa.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.elsevier.com/Keywords: Hirsutella, Morphological plasticity, Molecular phylogenetics, Anamorph-teleomorph connection, CordycepsKeywords: Hirsutella, Morphological plasticity, Molecular phylogenetics, Anamorph-teleomorph connection, Cordycep

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045The ability of a fungus to infect novel hosts is dependent on changes in gene content, expression, or regulation. Examining gene expression under simulated host conditions can explore which genes may contribute to host jumping. Insect pathogenesis is the inferred ancestral character state for species of Tolypocladium, however several species are parasites of truffles, including Tolypocladium ophioglossoides. To identify potentially crucial genes in this interkingdom host switch, T. ophioglossoides was grown on four media conditions: media containing the inner and outer portions of its natural host (truffles of Elaphomyces), cuticles from an ancestral host (beetle), and a rich medium (Yeast Malt). Through high-throughput RNASeq of mRNA from these conditions, many differentially expressed genes were identified in the experiment. These included PTH11-related G-protein-coupled receptors (GPCRs) hypothesized to be involved in host recognition, and also found to be upregulated in insect pathogens. A divergent chitinase with a signal peptide was also found to be highly upregulated on media containing truffle tissue, suggesting an exogenous degradative activity in the presence of the truffle host. The adhesin gene, Mad1, was highly expressed on truffle media as well. A BiNGO analysis of overrepresented GO terms from genes expressed during each growth condition found that genes involved in redox reactions and transmembrane transport were the most overrepresented during T. ophioglossoides growth on truffle media, suggesting their importance in growth on fungal tissue as compared to other hosts and environments. Genes involved in secondary metabolism were most highly expressed during growth on insect tissue, suggesting that their products may not be necessary during parasitism of Elaphomyces. This study provides clues into understanding genetic mechanisms underlying the transition from insect to truffle parasitism

Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus

Using spatial autocorrelation analysis, we examined the within-population genetic structure of Rhizopogon vinicolor and R. vesiculosus, two hypogeous ectomycorrhizal (EM) species that are sympatric sister taxa known to differ in their clonal structure. We collected 121 sporocarps and 482 tuberculate EM of both species from a 20 ha forest stand dominated by Douglas-fir (Pseudotsuga menziesii). Field collections were identified to species with restriction fragment length polymorphism analysis of the nuclear ribosomal internal transcribed spacer. Five and six microsatellite markers were used to characterize the genetic diversity of EM and sporocarp samples from R. vesiculosus and R. vinicolor respectively. After correcting for genet structure, spatial autocorrelation analyses of the EM samples were used to test the null hypothesis that multilocus genotypes characterized from each species were randomly distributed within the study area. We detected positive and statistically significant fine-scale genetic structure up to 120 m within the R. vesiculosus sample. In contrast, no spatial genetic structure was evident for R. vinicolor, indicating that the genotypes characterized for this species were randomly distributed throughout the study area. Differences in statistical power or the nuclear count of basidiospores are unlikely agents of the genetic patterns observed. Our results suggest that differences in reproductive output or competitive ability may act individually or in combination to create clusters of similar genotypes for R. vesiculosus throughout the study area.This is the publisher’s final pdf. The published article is copyrighted by the Mycological Society of America and can be found at: http://www.msafungi.org/Keywords: genet, Rhizopogon, ectomycorrhizal, genetic structure, spatial autocorrelation, fung