RPB2 Dataset Research Articles

Living with bats: polyphasic approach reveals a new Fusarium species in Yunnan Province, China

ABSTRACT Bats are one of the most diverse mammal groups, with over 1400 species distributed across the planet, and they provide key ecological and economic services. In addition, bats provide an ideal habitat for fungal growth and harbour a high diversity of fungal species. Previous studies have described 423 fungal species associated with bats and bat carcasses. This paper describes a new fungal species, Fusarium rhinolophi, belonging to Nectriaceae, collected from bats in Mengla County, Xishuangbanna Dai Autonomous Prefecture, Yunnan Province, China. Phylogenetic analyses of the combined ITS, CAM, TEF-1α, TUB, RPB1, and RPB2 dataset confirmed that our fungus forms an independent lineage within the F. nisikadoi species complex. Thus, we describe our fungus as a new species of Fusarium based on morphology and molecular phylogeny. A description, phylogenetic tree showing species placement, and micrographs are provided.

Identification of a new species and three new records of Chaetomiaceae associated with commercial herbal teas in northern Thailand

This study aimed to identify fungi associated with commercial herbal teas from local markets in Chiang Rai and Chiang Mai, Thailand. A new species, Arcopilus albae was isolated from mulberry leaf tea and identified based on evidence from molecular phylogenetic analysis. Phylogenetic analysis of a combined ITS, LSU, TUB2, and RPB2 dataset indicated that the new species is a distinct taxon with high statistical support. Furthermore, two isolates of Canariomyces arenarium and three isolates of Chaetomium globosum are described as new host records from five different commercial herbal teas (black and red goji berries, chrysanthemum flower, mulberry leaf, and stevia leaf). One isolate of Ch. rectangulare is described as a new host record from black goji berry and a new geographical record from northern Thailand. This study provides additional collections of fungi associated with dried commercial herbal tea products from local markets in the North of Thailand.

Phylogenetic and taxonomic appraisal of Neomanoharachariella xizangensis sp. nov. and the first asexual report of Acanthostigmina (Tubeufiaceae, Tubeufiales) from Xizang Autonomous Region, China

Tubeufiaceae species have diverse morphologies and habitats and are distributed in both tropical and temperate regions. In the past decade, several new and interesting Tubeufiaceae species were reported from China in aquatic and terrestrial habitats. In this study, we investigated two saprobic species collected on decaying wood in a terrestrial habitat of Xizang Autonomous Region, China. Through phylogenetic analyses of a combined ITS, LSU, tef1-α, and rpb2 dataset coupled with detailed morphological examinations, a novel species within Neomanoharachariella was identified. Phylogenetic analyses revealed that this new species formed a sister clade to Neomanoharachariella aquatica, but can be morphologically distinguished by its pale brown, septate, and flexuous conidiophores, alongside dark brown setae that turn hyaline at the apex and distinct muriform conidia. In addition, this study presents the first asexual and geographical record of Acanthostigmina (A. multiseptatum) from China. Acanthostigmina multiseptatum is characterized by micronematous, hyaline, and septate conidiophores with unique pleurogenous and helicoid conidia.

The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered.

Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia andFomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS +TEF1, ITS +TEF1 +RPB1 and ITS +TEF1 +RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided.

Storage Fungi and Mycotoxins Associated with Rice Samples Commercialized in Thailand.

The study focused on the examination of the different fungal species isolated from commercial rice samples, applying conventional culture techniques, as well as different molecular and phylogenic analyses to confirm phenotypic identification. Additionally, the mycotoxin production and contamination were analyzed using validated liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 40 rice samples were obtained covering rice berry, red jasmine rice, brown rice, germinated brown rice, and white rice. The blotting paper technique applied on the 5 different types of rice samples detected 4285 seed-borne fungal infections (26.8%) for 16,000 rice grains. Gross morphological data revealed that 19 fungal isolates belonged to the genera Penicillium/Talaromyces (18 of 90 isolates; 20%) and Aspergillus (72 of 90 isolates; 80%). To check their morphologies, molecular data (fungal sequence-based BLAST results and a phylogenetic tree of the combined ITS, BenA, CaM, and RPB2 datasets) confirmed the initial classification. The phylogenic analysis revealed that eight isolates belonged to P. citrinum and, additionally, one isolate each belonged to P. chermesinum, A. niger, A. fumigatus, and A. tubingensis. Furthermore, four isolates of T. pinophilus and one isolate of each taxon were identified as Talaromyces (T. radicus, T. purpureogenum, and T. islandicus). The results showed that A. niger and T. pinophilus were two commonly occurring fungal species in rice samples. After subculturing, ochratoxin A (OTA), generated by T. pinophilus code W3-04, was discovered using LC-MS/MS. In addition, the Fusarium toxin beauvericin was detected in one of the samples. Aflatoxin B1 or other mycotoxins, such as citrinin, trichothecenes, and fumonisins, were detected. These preliminary findings should provide valuable guidance for hazard analysis critical control point concepts used by commercial food suppliers, including the analysis of multiple mycotoxins. Based on the current findings, mycotoxin analyses should focus on A. niger toxins, including OTA and metabolites of T. pinophilus (recently considered a producer of emerging mycotoxins) to exclude health hazards related to the traditionally high consumption of rice by Thai people.

Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordycepsnujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China.

Ophiocordyceps contains the largest number of Cordyceps sensu lato, various species of which are of great medicinal value. In this study, a new entomopathogenic fungus, Ophiocordycepsnujiangensis, from Yunnan in southwestern China, was described using morphological, phylogenetic, and mitogenomic evidence, and its fungal community composition was identified. It was morphologically characterized by a solitary, woody, and dark brown stromata, smooth-walled and septate hyphae, solitary and gradually tapering conidiogenous cells with plenty of warty protrusions, and oval or fusiform conidia (6.4-11.2 × 3.7-6.4 µm) with mucinous sheath. The phylogenetic location of O.nujiangensis was determined based on the Bayesian inference (BI) and the maximum likelihood (ML) analyses by concatenating nrSSU, nrLSU, tef-1a, rpb1, and rpb2 datasets, and ten mitochondrial protein-coding genes (PCGs) datasets (atp6, atp9, cob, cox2, nad1, nad2, nad3, nad4, nad4L, and nad5). Phylogenetic analyses revealed that O.nujiangensis belonged to the Hirsutellasinensis subclade within the Hirsutella clade of Ophiocordyceps. And O.nujiangensis was phylogenetically clustered with O.karstii, O.liangshanensis, and O.sinensis. Simultaneously, five fungal phyla and 151 fungal genera were recognized in the analysis of the fungal community of O.nujiangensis. The fungal community composition differed from that of O.sinensis, and differences in the microbial community composition of closely related species might be appropriate as further evidence for taxonomy.

A Review of the Fungi That Degrade Plastic.

Plastic has become established over the world as an essential basic need for our daily life. Current global plastic production exceeds 300 million tons annually. Plastics have many characteristics such as low production costs, inertness, relatively low weight, and durability. The primary disadvantage of plastics is their extremely slow natural degradation. The latter results in an accumulation of plastic waste in nature. The amount of plastic waste as of 2015 was 6300 million tons worldwide, and 79% of this was placed in landfills or left in the natural environment. Moreover, recent estimates report that 12,000 million tons of plastic waste will have been accumulated on the earth by 2050. Therefore, it is necessary to develop an effective plastic biodegradation process to accelerate the natural degradation rate of plastics. More than 400 microbes have been identified as capable of plastic degradation. This is the first paper of the series on plastic-degrading fungi. This paper provides a summary of the current global production of plastic and plastic waste accumulation in nature. A list is given of all the plastic-degrading fungi recorded thus far, based on the available literature, and comments are made relating to the major fungal groups. In addition, the phylogenetic relationships of plastic-degrading fungi were analyzed using a combined ITS, LSU, SSU, TEF, RPB1, and RPB2 dataset consisting of 395 strains. Our results confirm that plastic-degrading fungi are found in eleven classes in the fungal phyla Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes, Saccharomycetes, and Sordariomycetes), Basidiomycota (Agaricomycetes, Microbotryomycetes, Tremellomycetes, Tritirachiomycetes, and Ustilaginomy-cetes), and Mucoromycota (Mucoromycetes). The taxonomic placement of plastic-degrading fungal taxa is briefly discussed. The Eurotiomycetes include the largest number of plastic degraders in the kingdom Fungi. The results presented herein are expected to influence the direction of future research on similar topics in order to find effective plastic-degrading fungi that can eliminate plastic wastes. The next publication of the series on plastic-degrading fungi will be focused on major metabolites, degradation pathways, and enzyme production in plastic degradation by fungi.

MALDI-TOF mass spectrometry–based identification of Eurotiales from different substrates and locations in Brazil

We used matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) fingerprinting to identify 95 strains of Aspergillus, Penicillium, and Talaromyces isolated from soil, marine sediment, and plants in Brazil. Samples for mass spectrometry were composed of conidia and conidiophores directly applied to the target plate and co-crystallized with the matrix solution. Cluster analyses of MS data and phylogenetic analyses based on the second largest subunit of RNA polymerase II gene sequence (RPB2) supported the identification of 42 species in Aspergillus (n = 17), Penicillium (n = 16), and Talaromyces (n = 9). In few cases, MALDI-TOF dendrograms split strains from one species into two neighboring clusters, but strains from different species were never grouped together. Three Penicillium species delimited by MALDI-TOF MS did not correspond to known species present in the large RPB2 dataset available for this group and may represent new taxa. These results expand the scope of applications of MALDI-TOF MS to the task of screening phylogenetically diverse assemblages of morphologically similar strains derived from field collections, allowing for fast discrimination of common and rare species, and detection of possible new taxa.

Multi-locus phylogeny reveals two new species of Exidia (Auriculariales, Basidiomycota) from China

Exidia glandulosa is a cosmopolitan species, and it was commonly reported from China. Seventeen specimens with close resemblance to the species by having blackish, gelatinous basidiocarps were analyzed based on morphological and molecular data. Phylogenetic analyses were performed by the combined ITS+nLSU dataset and the combined ITS+nLSU+TEF1-a + RPB2 dataset, and 20 ITS, 20 nLSU, 22 TEF1-a, and 20 RPB2 sequences were newly generated. Seventeen specimens were gathered into three different lineages in phylogenies, and they were identified as three species, E. glandulosa s. str. and two new species, E. reflexa and E. subglandulosa, respectively. The two new species differ from E. glandulosa s. str. by the absence of papillae on hymenial surface, and E. reflexa differs from E. subglandulosa by obvious effused-reflexed basidiocarps and smaller basidia and basidiospores. Detailed characteristics with morphological photos of two new species were provided here.

Two new species of Fuscoporia (Hymenochaetales, Basidiomycota) from southern China based on morphological characters and molecular evidence.

Fuscoporia (Hymenochaetaceae) is characterized by annual to perennial, resupinate to pileate basidiocarps, a dimitic hyphal system, presence of hymenial setae, and hyaline, thin-walled, smooth basidiospores. Phylogenetic analyses based on the nLSU and a combined ITS, nLSU and RPB2 datasets of 18 species of Fuscoporia revealed two new lineages that are equated to two new species; Fuscoporia ramulicolasp. nov. grouped together with F. ferrea, F. punctatiformis, F. subferrea and F. yunnanensis with a strong support; Fuscoporia acutimarginatasp. nov. formed a strongly supported lineage distinct from other species. The individual morphological characters of the new species and their related species are discussed. A key to Chinese species of Fuscoporia is provided.

Tylopilus griseiolivaceus sp. nov. and T. leucomycelinus (Boletaceae) revisited from the Dominican Republic within a comprehensive phylogeny of Tylopilus s. str.

The genus Tylopilus s. str. in the Dominican Republic is investigated. Tylopilus griseiolivaceus is introduced as a novel species based on material recorded in a neotropical montane pine woodland but also known to occur in temperate coniferous forests in southeastern USA. The Central American species T. leucomycelinus is also re-evaluated and its geographical range expanded. A detailed morphological description is provided for both species and accompanied by colour images of fresh basidiomes in habitat, line drawings of the main anatomical features and molecular support relying on a multilocus phylogenetic inference (nrITS, nrLSU (28S), rpb2 datasets). In addition, DNA was successfully isolated from the type material of T. leucomycelinus and compared with the genetic material obtained from additional neotropical samples. The taxonomic placement, ecological requirements and distribution patterns of T. griseiolivaceus and T. leucomycelinus are investigated/reviewed and their relationships with closely allied taxa in Tylopilus s. str. are elucidated and discussed. Epitypification of T. leucomycelinus is proposed herein.

Heterobasidion amyloideopsis sp. nov. (Basidiomycota, Russulales) evidenced by morphological characteristics and phylogenetic analysis

Heterobasidion amyloideopsis sp. nov., a new poroid wood-inhabiting species from Pakistan, is introduced based on a combination of molecular evidence and morphological characteristics. We generated sequences from the nuclear internal transcribed spacer regions (ITS) and the large subunit ribosomal RNA gene (LSU), the gene encoding the largest subunit of RNA polymerase II (RPB1) and the second subunit of RNA polymerase II (RPB2), focusing on two specimens from Pakistan. We performed phylogenetic analyses with maximum likelihood, maximum parsimony, and bayesian inference methods on two datasets (RPB1+RPB2 and ITS+nLSU+RPB1+RPB2). Both analyses supported the existence of the new species and showed that it formed a monophyletic group within the H. insulare complex as a sister to H. amyloideum. In addition to assessing the origin and divergence of this new species, we focused on the RPB1+RPB2 dataset to perform maximum likelihood based estimation and Bayesian binary analyses. Heterobasidion amyloideopsis is characterized by an annual habit, pileate basidiomata with a rust colored pileal surface, white, obtuse margin, a dimitic hyphal system with simple septate generative hyphae in the trama and clamp connections present on the contextual hyphae, amyloid skeletal hyphae and broadly ellipsoid, hyaline, fairly thick-walled, and asperulate basidiospores.

Clitolyophyllum akcaabatense gen. nov., sp. nov. (Agaricales, Tricholomatineae); a new fan-shaped clitocyboid agaric from Turkey

Clitolyophyllum akcaabatense gen. nov., sp. nov., is described based on both morphological and molecular data from Akcaabat, Trabzon, Turkey. Its characterizing features are a fan-shaped pileus, an eccentric and fibrillose stipe, 2–4 spored basidia, smooth, ellipsoid, and inamyloid white basidiospores, and growth on the bark of Picea orientalis (L.) Link. Phylogeny based on multigene molecular analysis (nrITS, nrLSU, rpb2 datasets) of the Tricholomatoid clade is provided. Photographs of fresh basidiomata and of the main micromorphological features are included.

New and noteworthy species of white Entoloma (Agaricales, Entolomataceae) in China

Three species of Entoloma with white basidioma in subgenus Alboleptonia from China are reported in this paper. Entoloma crocotillum is described as new to science from high altitudes in southwestern China. It is characterized by the small, white to pinkish pileus covered with matted-appressed fibrils, relatively large basidiospores with 5–6 angles, and the common presence of clamp-connections. Entoloma sulcatum, a new Chinese record, and E. stylophorum are documented based on new collections. Additionally, ITS (internal transcribed spacer region), nLSU (nuclear large subunit), and RPB2 (RNA polymerase II second largest subunit) sequences of E. crocotillum were successfully generated, and the phylogenetic positions of the three species among Alboleptonia species and other entolomatoid groups are preliminarily analyzed based on the combined nLSU and RPB2 dataset. The phylogenetic analysis showed that E. crocotillum is most closely related to E. sericellum and that Alboleptonia is not a monophyletic group.

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.

Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi)

The Sordariomycetes is an important group of fungi whose taxonomic relationships and classification is obscure. There is presently no multi-gene molecular phylogeny that addresses evolutionary relationships among different classes and orders. In this study, phylogenetic analyses with a broad taxon sampling of the Sordariomycetes were conducted to evaluate the utility of four gene regions (LSU rDNA, SSU rDNA, beta-tubulin and RPB2) for inferring evolutionary relationships at different taxonomic ranks. Single and multi-gene genealogies inferred from Bayesian and Maximum Parsimony analyses were compared in individual and combined datasets. At the subclass level, SSU rDNA phylogenies demonstrate their utility as a marker to infer phylogenetic relationships at higher levels. All analyses with SSU rDNA alone, combined LSU rDNA and SSU rDNA, and the combined 28 S rDNA, SSU rDNA and RPB2 datasets resulted in three subclasses: Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae, which correspond well to established morphological classification schemes. At the ordinal level, the best resolved phylogeny was obtained from the combined LSU rDNA and SSU rDNA datasets. Individually, the RPB2 gene dataset resulted in significantly higher number of parsimony informative characters. Our results supported the recent separation of Boliniaceae, Chaetosphaeriaceae and Coniochaetaceae from Sordariales and placement of Coronophorales in Hypocreomycetidae. Microascales was found to be paraphyletic and Ceratocystis is phylogenetically associated to Faurelina, while Microascus and Petriella formed another clade and basal to other members of Halosphaeriales. In addition, the order Lulworthiales does not appear to fit in any of the three subclasses. Congruence between morphological and molecular classification schemes is discussed.