Duplex Context Research Articles

Neomensularia meridionalis sp. nov. (Hymenochaetales, Basidiomycota), a New Species from South America

During field surveys in the Atlantic Forest of Southern Brazil, specimens of a poroid and pileate species of Hymenochaetaceae were found and are described as a new species, Neomensularia meridionalis. This species is morphologically and phylogenetically (ITS and nLSU) close to Neomensularia crocitincta, distributed in Central America, Cuba and Jamaica, but can be distinguished by its larger basidiomata, a duplex context featuring a distinct black line, and golden yellow basidiospores. Additionally, an updated identification key for Neomensularia species worldwide is provided.

Fulvifomes aurantiacus sp. nov. (Basidiomycota; Hymenochaetaceae) from Pakistan

The present study is the first report dealing with Pakistani Fulvifomes species. A new species, Fulvifomes aurantiacus, is identified on the basis of morpho-anatomical and phylogenetic analyses from Lahore, Pakistan. The species is characterized by pileate to sub-stipitate, basidiocarps having orange-brown pileal surface with yellow ocher wide zones and velutinous poroid hymenophore; 4–5 pores per millimeter, the presence of duplex context, dimitic hyphal system, absence of hymenial setae and the presence of contextual gleoplerous hyphae and highly pigmented ovoid to sub-globose basidiospores, 4.4–6.7 × 3.75–5.8 μm. Phylogenetically, our species formed a distinct clade with other Fulvifomes species, indicating its distinct position in the genus.

Two new stipitate species of Phylloporia (Basidiomycota, Hymenochaetaceae) from Chamela Biology Station, U.N.A.M. in Jalisco, Mexico

Phylloporia species are characterized by having annual to perennial, with resupinate, pileate-sessile to pileate-stipitate basidiomata, and duplex context. They have monomitic to dimitic hyphal system, basidiospores are globose to cylindrical, thick-walled, yellowish to pale brown in KOH. The genus includes 72 species described worldwide, and only eight taxa have been recorded in Mexico, five of which have been molecularly characterized. The objective of this study is to describe and illustrate two new stipitate species of Phylloporia from the Chamela Biology Station located in the municipality of La Huerta in the state of Jalisco, Mexico: P. rajchenbergii and P. ryvardenii. For this, the specimens were reviewed in detail in order to describe their macroscopic and microscopic characteristics, DNA extraction was performed and the 28S rDNA (LSU) was amplified by PCR. Phylogenetic analyzes were performed using Bayesian Inference and Maximum Likelihood methods. It is corroborated that Phylloporia rajchenbergii and P. ryvardenii differ from the species described in the genus due to the color of the pileus, the size of the pores, the type of context (homogeneous in P. ryvardenii) and the size of the basidiospores; in addition, both species form different clades in the phylogenetic analyzes carried out.

Ganodermaovisporum sp. nov. (Polyporales, Polyporaceae) from Southwest China.

Ganoderma is a white-rot fungus with a cosmopolitan distribution and includes several economically important species. This genus has been extensively researched due to its beneficial medicinal properties and chemical constituents with potential nutritional and therapeutic values. Traditionally, species of Ganoderma were identified solely based on morphology; however, recent molecular studies revealed that many morphology-based species are conspecific. Furthermore, some type species are in poor condition, which hinders us from re-examining their taxonomic characteristics and obtaining their molecular data. Therefore, new species and fresh collections with multigene sequences are needed to fill the loopholes and to understand the biological classification system of Ganoderma. In a survey of Ganoderma in Guizhou Province, southwest China, we found a new species growing on soil and, herein, it was identified by both morphology and phylogenetic evidence. Hence, we propose a new species, Ganodermaovisporum sp. nov. This species is characterised by an annual, stipitate, laccate basidiome, with a red-brown to brownish-black pileus surface and pale white pores, duplex context, clavate pileipellis terminal cells, trimitic hyphal system, ellipsoid basidiospores with dark brown eusporium bearing coarse echinulae and an obtuse turgid appendix. Phylogenetic analyses confirmed that the novel species sisters to G.sandunense with high bootstrap support. Furthermore, the RPB2 sequence of G.sandunense is supplied for the first time. Notably, we re-examined the type specimen of G.sandunense and provide a more precise description of the duplex context, pileipellis terminal cells and basidia. All species collected are described and illustrated with coloured photographs. Moreover, we present an updated phylogeny for Ganoderma, based on nLSU, ITS, RPB2 and TEF1-α DNA sequence data and species relationships and classification are discussed.

Two new species of Phylloporia (Hymenochaetales) from the Neotropics.

Two new species of Phylloporia, P.crystallina and P.sumacoensis, are described based on 28S ribosomal RNA phylogeny, morphology, host, and geographic distribution. Phylloporiacrystallina is characterized by pileate, perennial basidiomata with a duplex context, small pores 9-10 per mm, a monomitic hyphal system, absence of cystidia and cystidioles, presence of large rhomboid crystals in tube trama, broadly ellipsoid to subglobose basidiospores measuring 2.8-3 × 2-2.3 μm, and growth on angiosperm stump. Phylloporiasumacoensis is characterized by pileate, perennial basidiomata with a duplex context, very small pores 10-12 per mm, a monomitic hyphal system, hyphae at dissepiment edges bearing fine crystals, presence of cystidioles, broadly ellipsoid to subglobose basidiospores measuring 3-3.7 × 2.1-2.8 μm, and growth on living liana.

Phylogenetic analyses and morphological characters reveal two new species of Ganoderma from Yunnan province, China.

Ganodermadianzhongensesp. nov. and G.esculentumsp. nov. are proposed as two new species based on both phenotypic and genotypic evidences. Ganodermadianzhongense is characterized by the stipitate basidiomata, laccate and oxblood red pileus, gray white pore surface, duplex context and broadly ellipsoid basidiospores (9.0–12.5 × 6.5–9.0 μm) with coarse interwall pillars. Ganodermaesculentum is characterized by its basidiomata with slender stipe, white pore surface, homogeneous pileus context, and slightly truncate, narrow basidiospores (8.0–12.5 × 5.0–8.0 µm). Phylogenetic analyses were carried out based on the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α) and the second subunit of RNA polymerase II (RPB2) sequence data. The illustrations and descriptions for the new taxa are provided.

Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T.

The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.

<p><strong><em>Phylloporia</em></strong><strong> <em>moricola</em> <em>sp. nov.</em> (Hymenochaetales, Basidiomycota) from China</strong></p>

Phylloporia moricola is described as a new species based on collections from Sichuan Province, China. All studied basidiocarps grow on trunks of Morus sp. This new species is supported by morphological features and phylogenetic analyses of DNA sequences inferred from a dataset of nuc 28S rDNA. P. moricola is characterized by having effused-reflexed to pileate basidiocarps, pores 7–9 per mm, duplex context with a black line when young, dimitic hyphal system, and brownish, slightly thick-walled basidiospores generally measuring 3.4–4 × 2.7–3.2 μm. Phylloporia moricola is phylogenetically most closely related to Phylloporia mori, that also occurs on Morus sp., but that species differs from P. moricola in having hymenial setae and larger basidiospores (4–4.8 × 3.1–3.8 μm).

Fulvifomes nonggangensis and F. tubogeneratus (Hymenochaetales, Basidiomycota): Two New Species from Southern China Based on Morphological and Molecular Evidences

Two new species of Fulvifomes are described from specimens collected in rainforests of Nonggang Nature Reserve of southern China, based on morphological characteristics and molecular phylogenetic analysis of the internal transcribed spacer (ITS) and nuclear large subunit ribosomal DNA (nLSU) sequences. Fulvifomes nonggangensis sp. nov. is characterized by perennial, sessile and solitary basidiocarps, applanate pileus, small cystidioles of 9.9–15.4 × 2.9–3.5 μm, large pores of 5–6 per mm, a dimitic hyphal system, and broadly ellipsoid basidiospores of 4.3–5.3 × 3.3–4.2 μm. F. tubogeneratus sp. nov. is characterized by perennial, sessile, and imbricate basidiocarps, a duplex context, small pores of 7–8 per mm, a dimitic hyphal system, and ovoid to subglobose basidiospores of 5.72 × 5.00 μm.

New species and a new record of Phylloporia from Benin

Species of the wood-decay genus Phylloporia (Hymenochaetaceae, Hymenochaetales, Basidiomycota) are widely distributed in the tropics. Phylloporia species are, however, morphologically and ecologically diverse, which makes morphology-based species identification challenging. In this study, we re-examined species of Phylloporia reported from Benin (West Africa). Using an integrative approach combining morphology, ecology, and phylogenetic analyses, we describe Phylloporia beninensis sp. nov. and report Phylloporia littoralis for the first time outside of its type locality. Phylloporia beninensis sp. nov. is characterized by its annual and imbricate basidiomata, duplex context with a black zone separating the upper context from the lower one, dimitic hyphal system, presence of cystidioles, basidia of 9–12 × 4–5 μm, and subglobose to ellipsoid basidiospores measuring 3–4.6 × 2.1–3.6 μm. Detailed descriptions with illustrations for the new species are provided. With the addition of the new species, 15 Phylloporia species are now known to occur in tropical Africa. Our discovery of a new Phylloporia species in Benin should stimulate further mycological investigations in tropical African ecosystems to discover other new polypore species. To facilitate further taxonomy studies on tropical African Phylloporia taxa, a key to the known tropical African species is provided.

An updated phylogeny and diversity of Phylloporia (Hymenochaetales): eight new species and keys to species of the genus

Phylloporia is shown to be monophyletic according to molecular sequence data. Morphologically, Phylloporia is characterized by annual or perennial basidiomata, a monomitic to dimitic hyphal system, generally presenting a duplex context, absence of setae, and abundant tiny, thick-walled and colored basidiospores. In this study, specimens from China and Brazil a priori identified to Phylloporia species were revised. Phylogenetic analysis based on the nuc 28S rDNA showed that they nested within the Phylloporia clade, in which they formed eight new terminal lineages. According to this result and additional morphological and ecological data (host relationships), these eight lineages are described as eight new species: Phylloporia atlantica, P. cystidiolophora, P. montana, P. perangusta, P. rattanicola, P. solicola, P. splendida, and P. subpulla. Detailed descriptions with illustrations are provided for these new species, and their relationships with similar or allied species are discussed. An identification key for all accepted 56 species with a synoptic description is provided, and two keys to neotropical and Asian Phylloporia species are also provided.

A new species of Onnia (Hymenochaetales, Basidiomycota) from Vietnam

A new species, Onnia kesiya, is described from South Vietnam on the basis of morphological characteristics and molecular phylogenetic evidence. It is characterized by distinct lateral stipe, relatively thin and duplex context, hooked hymenial setae, widest basidiospores among Onnia species, and grows on Pinus kesiya in tropical pine forest. Detailed description with a photo and illustration is provided for the new species, and its relationships with similar species are discussed.

Phylloporia lonicerae (Hymenochaetales, Basidiomycota), a new species on Lonicera japonica from Japan and an identification key to worldwide species of Phylloporia.

Phylloporia, in the Hymenochaetaceae, is a polypore genus with a worldwide distribution. The new taxon Phylloporia lonicerae is introduced, which is the first Phylloporia species to originate from Japan. This species grows exclusively on living Lonicera japonica and is distinguished by annual, sessile basidiocarps that occur in clusters, pileal surface of narrow, concentrically sulcate zones, 6–8 pores per mm, duplex context separated by a black zone, dimitic hyphal system and broadly ellipsoid basidiospores, 3.2–4 × 2.3–3.1 µm. Phylogenetically, P. lonicerae is nested within the Phylloporia clade as a distinct terminal lineage with full statistical supports and sister to the clade of P. minutispora, P. cf. pulla and P. terrestris with weak supports. Besides Phylloporia bibulosa, P. chrysites and P. spathulata, P. lonicerae is the fourth species of Phylloporia recorded from Japan. An identification key to all accepted 48 species of Phylloporia is provided.

Phylloporia lespedezae sp. nov. (Hymenochaetaceae, Basidiomycota) from China

A new species, Phylloporia lespedezae, is described from Shanxi Province on the basis of morphological, ecological characters and molecular evidence. It is characterized by having an annual, pileate basidiocarps with wavy edge, duplex context separated by a black line, a monomitic hyphal system with simple septate generative hyphae, the presence of fusoid cystidioles, yellowish, broadly ellipsoid, thick-walled basidiospores, and growing on Lespedeza (Fabaceae) only. Phylogenetic analysis based on nuclear large subunit ribosomal DNA (nLSU) strongly support P. lespedezae as a distinct species within the genus of Phylloporia. Detailed description with illustration is provided for the new species and its relationships with similar species are discussed. In addition, a key to all 41 species of Phylloporia is provided.

Global diversity and phylogeny of Onnia (Hymenochaetaceae) species on gymnosperms

ABSTRACTOnnia includes white rotting polypores with annual basidiocarps, a duplex context, monomitic hyphal structure, hymenial setae, and hyaline, thin-walled, smooth basidiospores. Specimens of Onnia, originating mainly from East Asia, Europe, and North America, were studied using both morphology and phylogenetic analyses. Our concatenated data set was derived from 25 collections and included (i) 25 nuc rDNA internal transcribed spacer region sequences (ITS1-5.8S-ITS2 = ITS), 17 generated in this study; and (ii) 14 nuc rDNA 28S rDNA sequences, including the D1–D2 domains, 11 of them generated in this study. The resulting maximum likelihood and Bayesian phylogenies recovered all sampled collections of Onnia as a well-supported clade. In this clade, three previously accepted species, viz., Onnia leporina, O. tomentosa, and O. triquetra, received strong support, whereas three additional lineages with strong support represent the new species described in this paper, O. subtriquetra, O. microspora, and O. tibetica. Of the six Onnia species occurring on gymnosperms, O. tomentosa and O. leporina grow mainly on Picea and have circumboreal distribution in the Northern Hemisphere. In contrast, other species that mostly grow on Pinus are geographically restricted to limited regions, viz., O. triquetra in Europe, O. subtriquetra in North America, and O. microspora and O. tibetica in Asia.

Morphology and phylogeny reveal a novel hydnoid taxon from India: Mycorrhaphoides stalpersii gen. and sp. nov

Mycorrhaphoides gen. nov. and Mycorrhaphoides stalpersii sp. nov. are described and defined based on morphological details and phylogenetic inference of a hydnoid macrofungus collected in Acharya Jagadish Chandra Bose Indian Botanic Garden, Howrah (India). It is characterized by stipitate basidiomata with duplex context in stipe, presence of multi‐clamped septa, and smooth and hyaline cystidia.

Neomensularia duplicata gen. et sp. nov. (Hymenochaetales, Basidiomycota) and two new combinations

Neomensularia (Hymenochaetaceae) is a new genus introduced for N. duplicata sp. nov. (generic type), N. crocitincta and N. kanehirae combs. nov., based on a combination of distinct morphological characters and phylogenetic analyses inferred from nuc rDNA partial 28S and ITS datasets. The new genus is characterized by annual, pileate, brown to fuscous basidiocarps, duplex context, dimitic hyphal structure, ventricose, and hooked hymenial setae, golden yellow, thick-walled, smooth basidiospores that are negative in both Melzer’s reagent and Cotton Blue and a growth habit in tropical forests. Neomensularia duplicata closely resembles Mensularia radiata by hooked hymenial setae, but M. radiata has a homogenous context, larger pores (5–7 per mm), monomitic hyphal structure, hyphoid setae, larger cyanophilic basidiospores and occurs in temperate forests. Central American specimens labeled as Inonotus crocitinctus and Asian specimens identified as Fulvifomes kanehirae were re-examined. The duplex context, hooked hymenial setae and colored basidiospores are similar to N. duplicata. Phylogenetic inferences based on 28S and ITS sequence data confirm their affinities with N. duplicata and result in the proposal of new combinations, Neomensularia crocitincta and N. kanehirae.

Synthesis, base pairing and structure studies of geranylated RNA.

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium. The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNAGluUUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon–anticodon interaction during ribosome binding.

The structure and duplex context of DNA interstrand crosslinks affects the activity of DNA polymerase η.

Several important anti-tumor agents form DNA interstrand crosslinks (ICLs), but their clinical efficiency is counteracted by multiple complex DNA repair pathways. All of these pathways require unhooking of the ICL from one strand of a DNA duplex by nucleases, followed by bypass of the unhooked ICL by translesion synthesis (TLS) polymerases. The structures of the unhooked ICLs remain unknown, yet the position of incisions and processing of the unhooked ICLs significantly influence the efficiency and fidelity of bypass by TLS polymerases. We have synthesized a panel of model unhooked nitrogen mustard ICLs to systematically investigate how the state of an unhooked ICL affects pol η activity. We find that duplex distortion induced by a crosslink plays a crucial role in translesion synthesis, and length of the duplex surrounding an unhooked ICL critically affects polymerase efficiency. We report the synthesis of a putative ICL repair intermediate that mimics the complete processing of an unhooked ICL to a single crosslinked nucleotide, and find that it provides only a minimal obstacle for DNA polymerases. Our results raise the possibility that, depending on the structure and extent of processing of an ICL, its bypass may not absolutely require TLS polymerases.

Phylloporia minutipora and P. radiata spp. nov. (Hymenochaetales, Basidiomycota) from China and a key to worldwide species of Phylloporia

Phylloporia is a monophyletic genus within the Hymenochaetaceae as recovered by nuclear large subunit ribosomal DNA (nLSU) sequences. According to the summarization of 38 species accepted in this genus, Phylloporia is characterized by an absence of setae and the presence of abundant thick-walled, colored and tiny basidiospores, although its other morphological characters are highly diverse. Nine herbarium specimens from China, fitting the morphological concept of Phylloporia, were morphologically and phylogenetically studied in detail. The phylogeny inferred from nLSU sequences shows that the nine specimens formed three terminal lineages within the Phylloporia clade. Two lineages being composed of four specimens from Hainan and three from Guizhou were newly described as Phylloporia minutipora and P. radiata, respectively. In Phylloporia, P. minutipora is distinct by a combination of annual, sessile and imbricate basidiocarps, distinctly concentrically sulcate pileal surface with obtuse margin, angular pores of 12–15 per mm, duplex context separated by a black zone, a dimitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3 × 2–2.5 μm, while P. radiata is distinct by a combination of annual, sessile and imbricate basidiocarps, faintly sulcate and radially striate pileal surface, sharp pileal margin, angular pores of 8–10 per mm, duplex context separated by a black zone, a monomitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3.5 × 2–2.5 μm. The third lineage, comprising two specimens from Hainan, was morphologically determined as Phylloporia pulla. This species was recently combined to Phylloporia based on only morphological characters, and the current study for the first time generated its molecular sequences for phylogenetic reference. A key to all 40 species of Phylloporia is provided.