RPB2 Data Research Articles

Molecular studies of Flavopunctelia and Punctelia species and their Trebouxia photobiont from the Himalayas, India

Flavopunctelia and Punctelia species collected from Pir Panjal Ranges of Himachal Pradesh, India were studied by morphological, chemical, and phylogenetic methods. Analyses based on a concatenated ITS and LSU data set, confirmed the position of the three Indian taxa within the Parmotrema-clade in Parmeliaceae. The morphology-based taxonomic study reiterated the presence of cryptic species in Flavopunctelia with highly similar morphological characters in different species. The type species, F. flaventior, formed a well-supported monophyletic clade adjacent to F. soredica. In Punctelia, P. borreri was also established as a unique lineage along with P. perreticulata. RPB1 data were not interpreted due to data deficiency. The ITS sequence data and analyses showed Trebouxia photobionts in all the parmelioid species; that of P. borreri was identified as T. gelatinosa, but the photobionts of F. flaventior formed an exclusive clade of an apparently undescribed species of Trebouxia, and the photobiont of F. soredica formed an unresolved basal clade to the Trebouxia sp. of F. flaventior.

Two new species of Cyclocybe (Agaricales, Tubariaceae) from China

Cyclocybe encompasses 12 species which are distributed worldwide. In this study, two new species named C. suberebia and C. dinggyensis are introduced from China. Phylogenetic analyses based on nrITS, nrLSU, tef1-α, and rpb2 data show their placement within Cyclocybe in two distinct lineages. Cyclocybe suberebia is characterized by its dark brown to light brown pileus, smaller spore size, clampless hyphae. Cyclocybe dinggyensis is characterized by a slender basidioma, tetrasporic basidia and clampless hyphae. Descriptions, colour photographs and line drawings of both new species are presented.

Rhexoacrodictys melanospora sp. nov. (Rhexoacrodictys, Pleurotheciales) from Yunnan, China

Based on the morphological and phylogenetic analyses, we introduce a new species, Rhexoacrodictys melanospora, collected on decaying wood from terrestrial habitats in Yunnan, China. Phylogenetic analyses based on the combination of four loci (LSU, SSU, ITS and RPB2 data) demonstrated high support for establishing a new species within Rhexoacrodictys. The morphological characteristics of R. melanospora and the differences compared with the members of Rhexoacrodictys are also given in detail herein.

Insights into the Tricholomatineae (Agaricales, Agaricomycetes): a new arrangement of Biannulariaceae and Callistosporium, Callistosporiaceae fam. nov., Xerophorus stat. nov., and Pleurocollybia incorporated into Callistosporium

A new classification of the taxa formerly ascribed to Biannulariaceae (≡ Catathelasmataceae), viz. Catathelasma (type), Callistosporium, Pleurocollybia, Macrocybe, Pseudolaccaria, Guyanagarika and Anupama is here proposed. Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes including ITS, 18S and 28S rDNA, tef1 and rpb2 data supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma, which is significantly related with Bonomyces and Cleistocybe. Biannulariaceae is therefore emended to include the clade formed by Catathelasma, Bonomyces and Cleistocybe. Consequently, the new family Callistosporiaceae is proposed to name the clade containing Callistosporium (= Pleurocollybia) and related genera. Species of Callistosporium with distant lamellae, long hygrophoroid basidia and large amygdaliform spores are accommodated in the new genus Xerophorus. Finally, the new species Callistosporium pseudofelleum and Macrocybe sardoa are described, Clitocybe hesleri and C. fellea are combined into Callistosporium and Pseudolaccaria, respectively, and Callistosporium olivascens var. donadinii is upgraded to species rank and combined into Xerophorus.

<p><strong><em>Iodosphaeria honghense </em></strong><strong>sp. nov<em>. </em>(Iodosphaeriaceae<em>, </em>Xylariales) from Yunnan Province, China</strong></p>

Iodosphaeria honghense sp. nov., collected from dead twigs of an unknown host in Honghe, Yunnan Province, China, is introduced based on morphological characteristics and phylogenetic analyses. Iodosphaeria honghense is distinct from other similar taxa in having cylindrical to allantoid, guttulate ascospores without a mucilaginous sheath. Maximum likelihood and Bayesian analyses based on combined LSU, ITS and RPB2 data matrix indicate that I. honghense forms a distinct lineage within the Iodosphaeriaceae. This study provides a detailed description and illustrations with morphological comparisons, and includes a key to accepted Iodosphaeria species.

Mythicomycetaceae fam. nov. (Agaricineae, Agaricales) for accommodating the genera Mythicomyces and Stagnicola, and Simocybe parvispora reconsidered.

The analysis of a combined dataset including 5.8S (ITS) rDNA, 18S rDNA, 28S rDNA, and rpb2 data from species of the Agaricineae (Agaricoid clade) supports a shared monophyletic origin of the monotypic genera Mythicomyces and Stagnicola. The new family Mythicomycetaceae, sister to Psathyrellaceae, is here proposed to name this clade, which is characterised, within the dark-spored agarics, by basidiomata with a mycenoid to phaeocollybioid habit, absence of veils, a cartilaginous-horny, often tapering stipe, which discolours dark brown towards the base, a greyish brown, pale hazel brown spore deposit, smooth or minutely punctate-verruculose spores without a germ pore, cheilocystidia always present, as metuloids (thick-walled inocybe-like elements) or as thin-walled elements, pleurocystidia, when present, as metuloids, pileipellis as a thin ixocutis without cystidioid elements, clamp-connections present everywhere, and growth on wood debris in wet habitats of boreal, subalpine to montane coniferous forests. Simocybe parvispora from Spain (two collections, including the holotype), which clusters with all the sequenced collections of Stagnicola perplexa from Canada, USA, France and Sweden, must be regarded as a later synonym of the latter.

Penicillium gravinicasei, a new species isolated from cave cheese in Apulia, Italy

Several species of the genus Penicillium were isolated during a survey of the mycobiota of Apulian cave cheeses ripened in a cave in Gravina di Puglia, Italy. A novel species, Penicillium gravinicasei, is described in Penicillium section Cinnamopurpurea. Its taxonomic novelty was determined using a polyphasic approach, combining phenotypic, molecular (β-tubulin, calmodulin, ITS and DNA dependent RNA polymerase) DNA sequences and mycotoxin production data. Phylogenetic analyses of the RPB2 data showed that isolates of the novel species form a clade most closely related to Penicillium cinnamopurpureum and P. parvulum with high bootstrap support. The fungus did not produce ochratoxin A, citrinin, patulin, sterigmatocystin or aflatoxin B1 on standard agar media. The novel species had a high growth rate on agar media supplemented with 5% NaCl, and could be distinguished from other Penicillium section Cinnamopurpurea species by phenotypic and molecular characteristics.

The Inocybe geophylla group in North America: a revision of the lilac species surrounding I. lilacina

ABSTRACTThe Inocybe geophylla group is circumscribed based on phylogenetic analysis of DNA sequences largely sampled from North America and Europe. Twenty-nine phylogenetic species are uncovered after analysis of combined nuc 28S rDNA (28S) and RNA polymerase II second largest subunit (rpb2) DNA sequence data. Species in the I. geophylla group share the presence of a cortina, silky-fibrillose pileus and stipe, pruinose stipe apex, spermatic odor, thick-walled hymenial cystidia, and smooth amygdaliform or elliptical basidiospores. Within the group, as many as five phylogenetic species attributable to I. lilacina and allies form a strongly supported clade based on analysis of nuc ITS1-5.8S-ITS2 rDNA (ITS [internal transcribed spacer]), 28S, and rpb2 data. However, all lilac-colored species do not form a monophyletic group. Sufficient morphological and ecological data are present to document four of the I. lilacina subgroup species, two of which are described from North America as new: I. ionocephala and I. sublilacina. Inocybe lilacina is recircumscribed based on sequencing the holotype and is distributed in the eastern United States under pines and/or hardwoods. Inocybe pallidicremea is a widespread and common conifer associate in mostly northern parts of North America, to which the name I. lilacina was previously applied. Descriptions, photographs, line drawings, and a taxonomic key to lilac species in the I. lilacina subgroup from North America are provided. Well-documented collections, especially notes on gross morphology and ecology, are needed to continue to assess and describe the high taxonomic variation in the I. lilacina subgroup and its allies worldwide.

Pseudoclitocybaceae fam. nov. (Agaricales, Tricholomatineae), a new arrangement at family, genus and species level

A new classification of several clitocyboid taxa is here proposed to accommodate results from multigenic phylogenetic inference. The analysis of ITS rDNA as well as a combined dataset including 18S and 28S rDNA, tef1 and rpb2 data, support significantly a shared monophyletic origin of the genera Pseudoclitocybe, Musumecia and Pogonoloma, and the species Clitocybe alexandri and C. harperi. The new family Pseudoclitocybaceae is here proposed to name this clade, characterized by the presence of loop-like clamp connections in most species, absence of cystidia, and parallel hymenophoral trama with broad, cylindrical hyphae with intracellular granulations. The new genera Clitopaxillus and Harmajaea are proposed to accommodate the type species C. alexandri and H. harperi, as well as the combination H. wellsiae. In addition, two new species are described: C. fibulatus has a differential distribution of clamp connections in the basidiome, while H. guldeniae is, by now, an exclusively European taxon with brownish pileus, somewhat decurrent gills, ovoid spores and basidia longer than those of H. harperi. Finally, the species concept within Pseudoclitocybe and Pogonoloma is discussed and descriptions of the most representative species are provided.

DISCOMYCETES: the apothecial representatives of the phylum Ascomycota

Discomycetes are an artificial grouping of apothecia-producing fungi in the phylum Ascomycota. Molecular-based studies have revealed that the discomycetes can be found among ten classes of Ascomycota. The classification of discomycetes has been a major challenge due to the lack of a clear understanding of the important morphological characters, as well as a lack of reference strains. In this review, we provide a historical perspective of discomycetes, notes on their morphology (including both asexual and sexual morphs), ecology and importance, an outline of discomycete families and a synoptical cladogram of currently accepted families in Ascomycota showing their systematic position. We also calculated evolutionary divergence times for major discomycetous taxa based on phylogenetic relationships using a combined LSU, SSU and RPB2 data set from 175 strains and fossil data. Our results confirm that discomycetes are found in two major subphyla of the Ascomycota: Taphrinomycotina and Pezizomycotina. The taxonomic placement of major discomycete taxa is briefly discussed. The most basal group of discomycetes is the class Neolectomycetes, which diverged from other Taphrinomycotina around 417 MYA (216–572), and the most derived group of discomycetes, the class Lecanoromycetes, diverged from Eurotiomycetes around 340 MYA (282–414). Further clarifications based on type specimens, designation of epitypes or reference specimens from fresh collections, and multi-gene analyses are needed to determine the taxonomic arrangement of many discomycetes.

Origin and Evolution of Allopolyploid Wheatgrass Elymus fibrosus (Schrenk) Tzvelev (Poaceae: Triticeae) Reveals the Effect of Its Origination on Genetic Diversity.

Origin and evolution of tetraploid Elymus fibrosus (Schrenk) Tzvelev were characterized using low-copy nuclear gene Rpb2 (the second largest subunit of RNA polymerase II), and chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Ten accessions of E. fibrosus along with 19 Elymus species with StH genomic constitution and diploid species in the tribe Triticeae were analyzed. Chloroplast trnL–trnF sequence data suggested that Pseudoroegneria (St genome) was the maternal donor of E. fibrosus. Rpb2 data confirmed the presence of StH genomes in E. fibrosus, and suggested that St and H genomes in E. fibrosus each is more likely originated from single gene pool. Single origin of E. fibrosus might be one of the reasons causing genetic diversity in E. fibrosus lower than those in E. caninus and E. trachycaulus, which have similar ecological preferences and breeding systems with E. fibrosus, and each was originated from multiple sources. Convergent evolution of St and H copy Rpb2 sequences in some accessions of E. fibrosus might have occurred during the evolutionary history of this allotetraploid.

Luteoamylascus aculeatus (Pezizomycetes, Pezizaceae): a new genus and species near the Pachyphlodes–Amylascus lineage

The new taxon Luteoamylascus aculeatus described in this article is proposed to accommodate two collections of a hypogeous ascomycete from central Spain, characterized by a tomentose yellowish peridium, labyrinth-like gleba filled with whitish hyphae, and intensely reacting amyloid asci. ITS, 28S, and RPB2 data suggest that this new taxon is an independent lineage proposed here as the new genus Luteoamylascus. Until now, this lineage was only known from ectomycorrhizal root tips and mitotic spore mats. In phylogenetic analyses, the Luteoamylascus lineage is placed close to the genera Amylascus, Pachyphlodes, and Scabropezia. Morphological data suggest an affinity with Amylascus.

Three New Species of Cyphellophora (Chaetothyriales) Associated with Sooty Blotch and Flyspeck.

The genus Cyphellophora includes human- and plant-related species from mammal skin and nails, plant materials, and food. On the basis of analysis of ITS, LSU, TUB2 and RPB1 data and morphological characters, three new species, Cyphellophora phyllostachysdis, C. artocarpi and C. musae, associated with sooty blotch and flyspeck disease, were added to this genus. The 2D structure of ITS1 and ITS2 confirmed this taxonomic status. Pathogenicity tests on apple fruit indicated that C. artocarpi could be a sooty blotch and flyspeck pathogen of apple.

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae).

To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus.

Four new Arthoniomycetes from Bwindi Impenetrable National Park, Uganda – supported by molecular data

Arthonia physcidiicola Frisch & G.Thor, Chiodecton sorediatum G.Thor & Frisch, Herpothallon kigeziense Frisch & G.Thor and Reichlingia syncesioides Frisch & G.Thor are described as new to science. All species have been collected in the montane rainforests of Bwindi Impenetrable National Park in south western Uganda. The earlier monotypic genus Reichlingia with one anamorphic species is emended to include three fertile species and is newly reported to Africa. The combinations Reichlingia virginea (Mull.Arg.) Frisch for Arthothelium virgineum Mull. Arg. from the Usambara Mts. in north eastern Tanzania, and Reichlingia zwackhii (Sandst.) Frisch & G.Thor for the European Arthonia zwackhii Sandst. are made. A phylogenetic tree based on Bayesian and ML analyses of combined mtSSU, nLSU and RPB2 data showing the position of the new species in Arthoniomycetes is presented.

Nucleotide divergence and genetic relationships of Pseudoroegneria species

Nucleotide variation in 8 diploid Pseudoroegneria species was characterized using two single copy nuclear genes, the second largest subunit of RNA polymerase II ( RPB2 ) and the translation elongation factor G ( EF-G ), and one chloroplast TrnD / T intergenic region. Among the Pseudoroegneria species studied, the estimates of nucleotide diversity ( π ) ranged from 0.04577 ( RPB2 ) and 0.00183 ( TrnD / T ) for Pseudoroegneria tauri to 0.10667 ( RPB2 ), 0.06174 ( EF-G ) and 0.03743 ( TrnD / T ) for Pseudoroegneria spicata . The highest nucleotide diversity of the RPB2 data set was found for P. spicata among the taxa analyzed. Our phylogenetic analyses separated the accessions of P. spicata into several groups, with 7 accessions of P. spicata forming a highly supported subclade (BS = 100%, PP = 1.00). The phylogenetic analysis also suggests that P. spicata , Pseudoroegneria gracillima and Pseudoroegneria stipifolia have a closer relationship than the other species within Pseudoroegneria . Pseudoroegneria libanotica and P. tauri were also found to exhibit a high level of sequence homology, however, only nuclear gene data ( RPB2 and EF-G ) clearly indicated the differentiation between the P. libanotica + P. tauri group with other St genome species. ► We characterized nucleotide variation in 8 diploid Pseudoroegneria species. ► The highest nucleotide diversity of the RPB2 was found for Pseudoroegneria spicata among the taxa analyzed. ► A close relationship among P. spicata , Pseudoroegneria gracillima and Pseudoroegneria stipifolia was revealed. ► Pseudoroegneria libanotica and Pseudoroegneria tauri were also found to exhibit a high level of sequence homology.

Parallel evolution and phenotypic divergence in lichenized fungi: A case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales)

A molecular phylogeny of combined mtSSU, nuLSU, and RPB2 data revealed previously unrecognized levels of parallel evolution and phenotypic divergence in the lichen family Graphidaceae. Five clades were supported within the family: the Fissurina, Ocellularia, Graphis, Topeliopsis, and Thelotrema clades, containing 33 of the 42 currently accepted genera within the family. The results for the first time provide a fully resolved phylogeny of this family and confirm the synonymy of Graphidaceae and Thelotremataceae. Ancestral character state reconstruction using likelihood, Bayesian, and parsimony approaches indicate that lirellate ascomata evolved independently in each of the five clades. Carbonized ascomata evolved independently in at least four of the five clades. An unexpected result was the independent evolution of columella structures in the Fissurina and Ocellularia clades. Besides these more general findings, we document several cases in which evolution of several traits in parallel resulted in striking look-alikes within unrelated lineages, such as Topeliopsismuscigena and Chapsameridensis in the Topeliopsis and Thelotrema clades, Leptotremawightii, Myriotremalaeviusculum, and Leucodectonphaeosporum in the Ocellularia and Thelotrema clades, Ocellulariastylothecia and Melanotremameiosporum in the Fissurina and Ocellularia clades, and Myriotremapycnoporellum, Myriotremaclandestinum and Wirthiotremaglaucopallens in the Fissurina, Ocellularia, and Topeliopsis clades. Pagel’s test of independent character evolution suggested that at least for some of the traits involved in these cases, ecological constraints may have caused their evolution in parallel. The most intriguing find is the correlation between gall-forming thalli and vertical columns of calcium oxalate crystals, suggesting that these crystals do not function as light distributors, as previously assumed, but instead stabilize the thalli which are usually hollow beneath, similar to a dome-shaped structure. Ancestral character state reconstruction together with an approach to visualize the phenotype of putative ancestral lineages suggested the alpha-Graphidaceae to resemble some of the extant species currently classified in Myriotrema s.lat., with pore-like ascomata, and non-amyloid ascospores with lens-shaped lumina.

Maternal origin, genome constitution and evolutionary relationships of polyploid Elymus species and Hordelymus europaeus

The trnS/psbC region of chloroplast DNA (cpDNA) was sequenced for 18 Elymus polyploid species, Hordelymus europaeus and their putative diploid ancestors. The objective was to determine the maternal origin and evolutionary relationships of these polyploid taxa. Phylogenetic analysis showed that Elymus and Pseudoroegneria species formed a highly supported monophyletic group (100 % bootstrap values), suggesting that Pseudoroegneria is the maternal genome donor to polyploid Elymus species studied here. The phylogenetic tree based on cpDNA sequence data indicates that E. submuticus contains a St-genome. Taking into consideration of our previously published RPB2 data, we can conclude that hexaploid E. submuticus contains at least one copy of St and Y genomes. Our Neighor-joining analysis of cpDNA data put Psathyrostachys juncea, Hordeum bogdanii and Hordelymus europaeus into one group, suggesting a close relationship among them.

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.

Molecular evolution and phylogeny of the RPB2 gene in the genus Hordeum

It is known that the miniature inverted-repeat terminal element (MITE) preferentially inserts into low-copy-number sequences or genic regions. Characterization of the second largest subunit of low-copy nuclear RNA polymerase II (RPB2) has indicated that MITE and indels have shaped the homoeologous RPB2 loci in the St and H genome of Eymus species in Triticeae. The aims of this study was to determine if there is MITE in the RPB2 gene in Hordeum genomes, and to compare the gene evolution of RPB2 with other diploid Triticeae species. The sequences were used to reconstruct the phylogeny of the genus Hordeum. RPB2 regions from all diploid species of Hordeum, one tetraploid species (H. brevisubulatum) and ten accessions of diploid Triticeae species were amplified and sequenced. Parsimony analysis of the DNA dataset was performed in order to reveal the phylogeny of Hordeum species. MITE was detected in the Xu genome. A 27-36 bp indel sequence was found in the I and Xu genome, but deleted in the Xa and some H genome species. Interestingly, the indel length in H genomes corresponds well to their geographical distribution. Phylogenetic analysis of the RPB2 sequences positioned the H and Xa genome in one monophyletic group. The I and Xu genomes are distinctly separated from the H and Xa ones. The RPB2 data also separated all New World H genome species except H. patagonicum ssp. patagonicum from the Old World H genome species. MITE and large indels have shaped the RPB2 loci between the Xu and H, I and Xa genomes. The phylogenetic analysis of the RPB2 sequences confirmed the monophyly of Hordeum. The maximum-parsimony analysis demonstrated the four genomes to be subdivided into two groups.