Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

Two new species of Trichoglossum (Geoglossaceae, Ascomycota) from south Mexico

Two new species of Trichoglossum are described from south Mexico based on morphological and molecular evidence. Trichoglossumcaespitosum is characterized by the caespitose ascomata, rough and coiled paraphyses and the ascospores with 9-11 septa. Trichoglossumtropicale is characterized by the capitate ascomata, clavate and straight paraphyses and the ascospores with 10-12 septa. Both species grow in the tropical forests of the Yucatán peninsula. Here we provide descriptions and photographs for these species, together with a phylogenetic analyses based on the DNA sequences of nuc rDNA (ITS region and 28S gene) and a comparative table for the species known for America.

Mitrula aurea sp. nov., A New Aero-Aquatic Species from the Republic of Korea

The genus Mitrula (Mitrulaceae, Helotiales), as also known as swamp beacons, inhabits submerged, decaying vegetation in standing or decaying needles, twigs, leaves, and shallow water. They play an important role in carbon cycling in some freshwater ecosystems. In the herbarium of the Korea National Arboretum (KH), seven Mitrula specimens were collected during mushroom forays in the period from 2019 to 2021. The Korean collections were found to be macromorphologically closely related to M. paludosa and M. elegans, but micromorphologically they could be distinguished by characteristics of slightly narrower asci and aseptate ascospores. Our molecular phylogenetic analyses of the internal transcribed spacer (ITS) and 28S rDNA regions also revealed that our specimens were related to M. paludosa and M. elegans, but formed a distinct clade. Based on these results, we reported our specimens as new to science and discussed the phylogeny and diversity of Mitrula species.

Ascodesmisrosicola sp. nov. and Talaromycesrosarhiza sp. nov., two endophytes from Rosaroxburghii in China

Background

Rosaroxburghii Tratt., a deciduous shrub of the family Rosaceae, is usually used as food and medicinal materials and also cultivated as an ornamental. Plant endophytic fungi are a large class of microbial resources not fully researched, with great potential applications. Two strains of Ascodesmis and Talaromyces were isolated during a survey of biodiversity on endophytic fungi of R.roxburghii in China. Multigene phylogenetic analyses showed that each of the two fungi formed a distinct lineage and separated from known congeneric species and they are proposed as two novel taxa.

New information

Ascodesmisrosicola sp. nov. usually has one or two conspicuous simple or branched ridges extending to the majority of the ascospore surface and remarkably small asci, distinguishing it from the previously-described species in the genus Ascodesmis. Talaromycesrosarhiza sp. nov., of the section Talaromyces, is closely related to T.francoae. It differs from the latter by having both monoverticillate and biverticillate conidiophores, while those of T.francoae are biverticillate. Both novel endophytes are illustrated and described.

Genetic variations and in vitro root-colonizing ability for an ericaceous host in Sarcoleotia globosa (Geoglossomycetes)

We discovered that Sarcoleotia globosa (Geoglossomycetes) fruited on the soil of ornamental Erica pot cultures, and its ascospores can germinate on plain agar. These findings prompted us to collect isolates from horticultural and natural environments in Japan and analyze their phylogeny and root colonizing ability. Pure cultures were successfully obtained from ascospores and surface-sterilized ericaceous roots. Phylogenetic analysis based on rRNA internal transcribed spacer sequences revealed that Japanese samples were separated into three strongly supported clades. Individual clade consisted of samples derived from (1) Erica pot cultures, (2) Rhododendron planted in a garden or Vaccinium pot culture, and (3) natural habitats in Hokkaido. Colony characteristics and in vitro root-colonizing morphology observed may correspond to these phylogenetic variations. Irrespective of the clades, all tested strains formed hyphal coils in vital rhizodermal cells of V. virgatum seedlings, which resembled those of ericoid mycorrhizae. Our results represent novel findings that can be the first step in unraveling the currently unknown ecology of geoglossoid fungi.

Antarctolichenia onofrii gen. nov. sp. nov. from Antarctic Endolithic Communities Untangles the Evolution of Rock-Inhabiting and Lichenized Fungi in Arthoniomycetes

Microbial endolithic communities are the main and most widespread life forms in the coldest and hyper-arid desert of the McMurdo Dry Valleys and other ice-free areas across Victoria Land, Antarctica. There, the lichen-dominated communities are complex and self-supporting assemblages of phototrophic and heterotrophic microorganisms, including bacteria, chlorophytes, and both free-living and lichen-forming fungi living at the edge of their physiological adaptability. In particular, among the free-living fungi, microcolonial, melanized, and anamorphic species are highly recurrent, while a few species were sometimes found to be associated with algae. One of these fungi is of paramount importance for its peculiar traits, i.e., a yeast-like habitus, co-growing with algae and being difficult to propagate in pure culture. In the present study, this taxon is herein described as the new genus Antarctolichenia and its type species is A. onofrii, which represents a transitional group between the free-living and symbiotic lifestyle in Arthoniomycetes. The phylogenetic placement of Antarctolichenia was studied using three rDNA molecular markers and morphological characters were described. In this study, we also reappraise the evolution and the connections linking the lichen-forming and rock-inhabiting lifestyles in the basal lineages of Arthoniomycetes (i.e., Lichenostigmatales) and Dothideomycetes.

The British chalk specialist Lecidea lichenicola auct. revealed as a new genus of Lichinomycetes

The lichen, to which the name Lecidea lichenicola is found to have been misapplied, was first described from England and is an extreme specialist of chalk pebbles. It has long been known that it is not closely related to Lecidea in the strict sense, but its true evolutionary relationships have been unknown. Here we use metagenome-assembled genome data to place this fungus in a six-locus phylogeny of Ascomycota, and find strong support for its placement in the class Lichinomycetes. Multiple gene trees using existing data from Lichinomycetes support its further placement within the family Lichinaceae. Based on a revision of types and original descriptions, we conclude that the earliest name for this species is Lecidea obsoleta (syn. Thrombium cretaceum). We neotypify that name by a modern collection and accommodate it in the new genus Watsoniomyces. Type and other original material of L. lichenicola (syn. Discocera lichenicola) was re-examined and found not to be on chalk and to represent a different lichen, Trapelia glebulosa. Watsoniomyces is the first described member of Lichinomycetes with an endolithic thallus.

Systematics, ecology, and application of Helotiales: Recent progress and future perspectives for research with special emphasis on activities within Japan

Helotiales is one of the most diverse groups of apothecial ascomycetes, including 3000-4000 taxa. Recent progress in the systematics, ecology, and their applications through research is herein reviewed based on the experiences of the author with a special emphasis on activities in Japan. In the past 30 y, more than 50 helotialean taxa have been added to the mycobiota of Japan, including new taxa. With the advent of molecular phylogeny, some families have been revisited, such as members with stroma (Sclerotiniaceae and Rutstroemiaceae) or hairs (Hyaloscyphaceae and Lachnaceae). Although the monophyly of Helotiales has not yet been demonstrated, our understanding of its phylogeny has greatly advanced. The unexpected ecological nature represented by endophytism has been revealed through barcoding and other molecular techniques. The research history of ash dieback is also reviewed, and the endophytism/saprophytism of the pathogen on its original host is discussed. Drug discoveries within Helotiales are reviewed, and successful examples are presented. As future perspectives, both the cumulation of occurrence and sequence data of Helotiales is greatly encouraged to elucidate this important group of fungi.

Revision of Xylonaceae (Xylonales, Xylonomycetes) to include Sarea and Tromera

The resinicolous fungi Sarea difformis and S. resinae (Sareomycetes) were taxonomically revised on the basis of morphological observations and phylogenetic analyses of the nucleotide sequences of the nSSU-LSU-rpb1-rpb2-mtSSU genes. The results of phylogenetic analyses show that S. difformis and S. resinae are grouped with members of Xylonomycetes. According to the results of phylogenetic analyses and their sexual and asexual morphs resemblance, Sareomycetes is synonymized with Xylonomycetes. Although Tromera has been considered a synonym of Sarea based on the superficial resemblance of the sexual morph, we show that they are distinct genera and Tromera should be resurrected to accommodate T. resinae (= S. resinae). Xylonomycetes was morphologically re-circumscribed to comprise a single family (Xylonaceae) with four genera (Sarea, Trinosporium, Tromera, and Xylona) sharing an endophytic or plant saprobic stage in their lifecycle, ascostroma-type ascomata with paraphysoid, Lecanora-type bitunicate asci, and pycnidial asexual morphs. Phylogenetic analyses based on ITS sequences and environmental DNA (eDNA) implied a worldwide distribution of the species. Although Symbiotaphrinales has been treated as a member of Xylonomycetes in previous studies, it was shown to be phylogenetically, morphologically, and ecologically distinct. We, therefore, treated Symbiotaphrinales as Pezizomycotina incertae sedis.

Sareomycetes cl. nov.: A new proposal for placement of the resinicolous genus Sarea (Ascomycota, Pezizomycotina)

Resinicolous fungi constitute a heterogeneous assemblage of fungi that live on fresh and solidified plant resins. The genus Sarea includes, according to current knowledge, two species, S. resinae and S. difformis. In contrast to other resinicolous discomycetes, which are placed in genera also including non-resinicolous species, Sarea species only ever fruit on resin. The taxonomic classification of Sarea has proven to be difficult and currently the genus, provisionally and based only on morphological features, has been assigned to the Trapeliales (Lecanoromycetes). In contrast, molecular studies have noted a possible affinity to the Leotiomycetes. Here we review the taxonomic placement of Sarea using sequence data from seven phylogenetically informative DNA regions including ribosomal (ITS, nucSSU, mtSSU, nucLSU) and protein-coding (rpb1, rpb2, mcm7) regions. We combined available and new sequence data with sequences from major Pezizomycotina classes, especially Lecanoromycetes and Leotiomycetes, and assembled three different taxon samplings in order to place the genus Sarea within the Pezizomycotina. Based on our data, none of the applied phylogenetic approaches (Bayesian Inference, Maximum Likelihood and Maximum Parsimony) supported the placement of Sarea in the Trapeliales or any other order in the Lecanoromycetes. A placement of Sarea within the Leotiomycetes is similarly unsupported. Based on our data, Sarea forms an isolated and highly supported phylogenetic lineage within the "Leotiomyceta". From the results of our multilocus phylogenetic analyses we propose here a new class, order, and family, Sareomycetes, Sareales and Sareaceae in the Ascomycota to accommodate the genus Sarea. The genetic variability within the newly proposed class suggests that it is a larger group that requires further infrageneric classification.

Continental-scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

PREMISE

Motivated to make sensible interpretations of the massive volume of data from the Australian Microbiome Initiative (AusMic), we characterize the soil mycota of Australia. We establish operational taxonomic units (OTUs) from the data and compare these to GenBank and a data set from the National Herbarium of Victoria (MEL), Melbourne, Australia. We also provide visualizations of Agaricomycete diversity, drawn from our analyses of the AusMic sequences and taxonomy.

METHODS

The AusMic internal transcribed spacer (ITS) data were filtered to create OTUs, which were searched against the National Center for Biotechnology Information Nucleotide database and the MEL database. We further characterized a portion of our OTUs by graphing the counts of the families and orders of Agaricomycetes. We also graphed AusMic species determinations for Australian Agaricomycetes against latitude.

RESULTS

Our filtering process generated 192,325 OTUs; for Agaricomycetes, there were 27,730 OTUs. Based on the existing AusMic taxonomy at species level, we inferred the diversity of Australian Agaricomycetes against latitude to be lowest between -20 and -25 decimal degrees.

DISCUSSION

BLAST comparisons provided reciprocal insights between the three data sets, including the detection of unusual root-associated species in the AusMic data, insights into mushroom morphology from the MEL data, and points of comparison for the taxonomic determinations between AusMic, GenBank, and MEL. This study provides a tabulation of Australian fungi, different visual snapshots of a subset of those taxa, and a springboard for future studies.

Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales

The class Laboulbeniomycetes comprises biotrophic parasites associated with arthropods and fungi. Two orders are currently recognized, Pyxidiophorales and Laboulbeniales. Herpomyces is an isolated genus of Laboulbeniales, with species that exclusively parasitize cockroaches (Blattodea). Here, we evaluate 39 taxa of Laboulbeniomycetes with a three-locus phylogeny (nrSSU, ITS, nrLSU) and propose a new order in this class. Herpomycetales accommodates a single genus, Herpomyces, with currently 26 species, one of which is described here based on morphological and molecular data. Herpomyces shelfordellae is found on Shelfordella lateralis cockroaches from Hungary, Poland, and the USA. We also build on the six-locus dataset from the Ascomycota Tree of Life paper (Schoch and colleagues, 2009) to confirm that Laboulbeniomycetes and Sordariomycetes are sister classes, and we apply laboulbeniomyceta as a rankless taxon for the now well-resolved node that describes the most recent common ancestor of both classes.

The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

A new species of Stamnaria (Leotiomycetes, Helotiales) from Western Siberia

A new species of Stamnaria is described based on morphology and molecular data from a collection made in West Siberia. Stamnariayugrana is differentiated by lanceolate, strongly protruding paraphyses and comparatively narrow, fusoid-clavate ascospores. The apothecia are urn-shaped due to a prominent and even collar as in S.persoonii. The species grows on fallen side branches of Equisetumsylvaticum, a rarely recorded host for Stamnaria. The authors formally describe the new species and provide colour illustrations. In addition, the literature is reviewed on previously described species of Stamnaria. Phylogenetic reconstruction of the Stamnaria lineage, based on the ITS ribosomal DNA, strongly supports the three currently recognised species: S.americana, S.persoonii and S.yugrana.

A plant pathology perspective of fungal genome sequencing

The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.

Taxonomic divergence of the green naked-stipe members of the genus Microglossum (Helotiales)

Four new species of the Ascomycete genus Microglossum are recognized, based on morphological characters and DNA sequences of nuc rDNA (ITS region and 28S gene) and the second largest subunit of RNA polymerase II (RPB2). They differ from Microglossum nudipes by the color of the ascocarps and the sizes and shapes of ascospores, asci, and paraphyses. A lectotype is proposed, and an emended description is provided for M. nudipes. Descriptions of new species Microglossum clavatum, M. truncatum, M. pretense, and M. tenebrosum are provided. Other closely related species in the group of green earth tongues include Microglossum viride, M. rickii, and M. griseoviride. An identification key to green Microglossum species is presented.

Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the "earth tongue fungi" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.

Re-evaluation of the morphological variability of Microglossum viride and M. griseoviride sp. nov

Studies in Microglossum viride (Pers.) Gillet revealed that the name was used incorrectly for two similar but different taxa. Analyses of morphological, ecological and molecular (sequences of ITS and LSU region of rRNA gene) characters of type and voucher specimens of M. viride and related taxa resulted in delimitation and description of a new species, Microglossum griseoviride V. Kučera, Lizoň & M. Tomšovský. Lectotypes of Geoglossum viride Pers., and epitype of Geoglossum viride are designated. Species Microglossum minus Velen. and Microglossum lutescens Boud. are confirmed to be conspecific to M. viride.

Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data

The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered.

Generic circumscriptions in Geoglossomycetes

The class Geoglossomycetes is a recently created class of Ascomycota, currently comprised of one family (Geoglossaceae) and five genera (Geoglossum, Nothomitra, Sarcoleotia, Thuemenidium and Trichoglossum). These fungi, commonly known as earth tongues, have long been a subject of mycological research. However, the taxonomy within the group has historically been hindered by the lack of reliable morphological characters, uncertain ecological associations, and the inability to grow these fungi in culture. The phylogenetic relationships of Geoglossomycetes were investigated by conducting maximum likelihood and Bayesian analyses using a 4-gene dataset (ITS, LSU, MCM7, RPB1). Five well-supported monophyletic clades were found that did not correspond exactly with the currently recognised genera, necessitating a taxonomic revision of the group. Two new genera are proposed: Glutinoglossum to accommodate G. glutinosum and the newly described species G. heptaseptatum, and Sabuloglossum to accommodate S. arenarium. The type species of Thuemenidium, traditionally included within the Geoglossaceae, is confirmed as belonging to a separate lineage that is only distantly related to Geoglossomycetes.

What an rRNA secondary structure tells about phylogeny of fungi in Ascomycota with emphasis on evolution of major types of ascus

Background

RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists.

Methodology/Principal Findings

We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes.

Conclusions

Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses.

Alternaria alternata allergen Alt a 1: a unique β-barrel protein dimer found exclusively in fungi

BACKGROUND

Alternaria species is one of the most common molds associated with allergic diseases, and 80% of Alternaria species-sensitive patients produce IgE antibodies to a major protein allergen, Alt a 1. The structure and function of Alt a 1 is unknown.

OBJECTIVE

We sought to obtain a high-resolution structure of Alt a 1 using x-ray crystallography and to investigate structural relationships between Alt a 1 and other allergens and proteins reported in the Protein Data Bank.

METHODS

X-ray crystallography was used to determine the structure of Alt a 1 by using a custom-designed set of crystallization conditions. An initial Alt a 1 model was determined by the application of a Ta(6)Br(12)(2+) cluster and single-wavelength anomalous diffraction. Bioinformatic analyses were used to compare the Alt a 1 sequence and structure with that of other proteins.

RESULTS

Alt a 1 is a unique β-barrel comprising 11 β-strands and forms a "butterfly-like" dimer linked by a single disulfide bond with a large (1345 Å(2)) dimer interface. Intramolecular disulfide bonds are conserved among Alt a 1 homologs. Currently, the Alt a 1 structure has no equivalent in the Protein Data Bank. Bioinformatics analyses suggest that the structure is found exclusively in fungi. Four previously reported putative IgE-binding peptides have been located on the Alt a 1 structure.

CONCLUSIONS

Alt a 1 has a unique, dimeric β-barrel structure that appears to define a new protein family with unknown function found exclusively in fungi. The location of IgE antibody-binding epitopes is in agreement with the structural analysis of Alt a 1. The Alt a 1 structure will allow mechanistic structure/function studies and immunologic studies directed toward new forms of immunotherapy for Alternaria species-sensitive allergic patients.

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.

Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny

Thuemenidium is a small earth tongue genus with three recognized white-spored species. Within Thuemenidium, T. atropurpureum and T. arenarium have been reported only from the northern hemisphere while T. berteroi is known solely in the southern hemisphere. We reviewed the ecology, examined the morphology and inferred the systematic positions of northern species of Thuemenidium from LSU-rDNA gene phylogeny of 48 taxa in Pezizomycotina including recent collections. Our results suggest that Thuemenidium in its current sense is polyphyletic and that T. atropurpureum, closely related to Microglossum and Leotia species, is a member of Leotiaceae (Helotiales, Leotiomycetes). Our phylogeny placed the other northern species, T. arenarium, in Geoglossaceae (Geoglossales, Geoglossomycetes), retaining genus Thuemenidium, pending further investigation.

Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta

We present a revised phylogeny of lichenised Dothideomyceta (Arthoniomycetes and Dothideomycetes) based on a combined data set of nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA data. Dothideomyceta is supported as monophyletic with monophyletic classes Arthoniomycetes and Dothideomycetes; the latter, however, lacking support in this study. The phylogeny of lichenised Arthoniomycetes supports the current division into three families: Chrysothrichaceae (Chrysothrix), Arthoniaceae (Arthonia s. l., Cryptothecia, Herpothallon), and Roccellaceae (Chiodecton, Combea, Dendrographa, Dichosporidium, Enterographa, Erythrodecton, Lecanactis, Opegrapha, Roccella, Roccellographa, Schismatomma, Simonyella). The widespread and common Arthonia caesia is strongly supported as a (non-pigmented) member of Chrysothrix. Monoblastiaceae, Strigulaceae, and Trypetheliaceae are recovered as unrelated, monophyletic clades within Dothideomycetes. Also, the genera Arthopyrenia (Arthopyreniaceae) and Cystocoleus and Racodium (Capnodiales) are confirmed as Dothideomycetes but unrelated to each other. Mycomicrothelia is shown to be unrelated to Arthopyrenia s.str., but is supported as a monophyletic clade sister to Trypetheliaceae, which is supported by hamathecium characters. The generic concept in several groups is in need of revision, as indicated by non-monophyly of genera, such as Arthonia, Astrothelium, Cryptothecia, Cryptothelium, Enterographa, Opegrapha, and Trypethelium in our analyses.