Nuclear Large Subunit Ribosomal RNA Research Articles

Three new species of Boletaceae from the Heishiding Nature Reserve in Guangdong Province, China

Based on morphological evidence and DNA sequencing, we propose three new species of the basidiomycete family Boletaceae, namely Aureoboletus venustus, Leccinellum onyx, and Pulveroboletus sinensis. The species were collected from the Heishiding Nature Reserve in Guangdong Province, China. The descriptions are illustrated by photographs and line drawings, and comparisons were made with related species. Morphologically, A. venustus is characterized by its mucilaginous pileus with red to reddish orange color, a vivid yellow hymenophore surface, and small ellipsoid basidiospores (7) 7.5–10.5 (12) × 5–6 (7) μm in size. Leccinellum onyx is characterized by its slightly areolating pileus with grayish orange to brownish orange color, a grayish brown to light grayish orange hymenophore surface, short yellowish white tubes, a yellowish white to brownish gray stipe covered with dark brown warts, and small ellipsoid basidiospores with a size of (8) 9–11 (12) × (4) 5–6 μm. Its nucleotide sequence of the internal transcribed spacer (ITS) region is particularly long (1080 bp) in comparison to related species. Pulveroboletus sinensis is characterized by its yellow to vivid yellow pulverulent pileus covered with deep orange to brownish orange conico-pyramidal scales, an appendiculate margin, greenish yellow tubes easily becoming cyanescent upon bruising, a yellow to vivid yellow stipe covered with yellow to brownish orange conico-floccose scales, and small smooth ellipsoid basidiospores with a size of (6) 6.5–8.5 (11) × (4.5) 5–6 (6.5) μm. Phylogenetic analysis of nucleotide sequences of the ITS region and the nuclear large subunit ribosomal RNA gene (nrLSU) provided further evidence that the described mushrooms represent new species.

Novel fungi from an ancient niche: lachnoid and chalara-like fungi on ferns

A survey was conducted in Brazil to collect fungi on ferns. Based on morphology and inferred phylogeny from DNA sequences of two loci, namely the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), several species belonging to chalara-like genera and lachnoid fungi were recognized. Eighteen fungal isolates, collected from five host species, representing 10 different localities were studied. Three novel genera (Lachnopsis, Scolecolachnum and Zymochalara), and six novel species (Bloxamia cyatheicola, Lachnopsis catarinensis, Lachnopsis dicksoniae, Scolecolachnum pteridii, Zymochalara lygodii and Zymochalara cyatheae) are introduced. Furthermore, two new combinations (Erioscyphella euterpes and Erioscyphella lushanensis) are proposed. Two novel taxa (Lachnopsis catarinensis and Lachnopsis dicksoniae) may be included in the list of potentially endangered fungal species in Brazil, if proven to be restricted to their tree-fern host, Dicksonia sellowiana, which is included in the official list of endangered plant species in Brazil.

Endogone corticioides sp. nov. from subalpine conifer forests in Japan and China, and its multi-locus phylogeny

Endogone corticioides sp. nov. was described from subalpine conifer forests in Japan and China. This species is similar to E. pisiformis in its yellowish sporocarps and zygosporangia on the equal empty gametangia. Endogone corticioides was clearly distinguished from E. pisiformis based on its resupinate sporocarp, the presence of hyphal peg-like structures on the peridium, and abundant thick-walled hyphae in the gleba. Phylogenetic analysis of the small and large subunit nuclear ribosomal RNA and the elongation factor-1α genes suggested that E. corticioides is closely related to E. pisiformis. Limited vegetative growth from the surface-sterilized sporocarps on agar media was shown.

Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales).

Bondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). From the results, we inferred that the maximum crown age of Bondarzewia is approximately 25.5 million-years-ago (Mya) and that tropical East Asia is likely to be its ancestral area, with three possible expansions leading to its distribution in North America, Europe and Oceania.

Phylogeny of Phyllophoraceae (Rhodophyta, Gigartinales) reveals Asterfilopsis gen. nov. from the Southern Hemisphere

:We investigated the phylogenetic position of Ahnfeltiopsis furcellata and Gymnogongrus disciplinalis from Peru and Chile using nuclear large-subunit ribosomal RNA, mitochondrial COI and plastid rbcL sequences and morphological examination. Both the combined (LSU + COI + rbcL) and rbcL data sets revealed that A. furcellata and G. disciplinalis consistently formed a clade with two Peruvian taxa. The form and development of the reproductive structures of these species supported the molecular phylogeny and underlined the fact that the clade of A. furcellata was distinct from other genera of Phyllophoraceae. We therefore describe Asterfilopsis gen. nov. and transfer A. furcellata and G. disciplinalis to the new genus. Asterfilopsis was characterised by (1) having medullary cells radially surrounded by clusters of carposporangia and connected to some of them, (2) the presence of ostioles instead of specialised carpostomata, and (3) the presence of terminal tubular gonimoblasts penetrating the cystocarp boundary. We also describe two new species, Asterfilopsis centralis and A. piurana, likely misidentified earlier as A. furcellata.

A new species of Skeletocutis (Polyporales, Basidiomycota) from Yunnan of China

A new species of Polyporales, named as Skeletocutis yunnanensis, was collected on angiosperm wood in northern Yunnan Province, southwestern China. It is described based on morphological characteristics and molecular evidence. The species belongs to the Skeletocutis subincarnata complex, but differs morphologically from all known species of the genus by white, cream to buff pores surface, angular pores mostly 5–6 per mm with entire mouths, a dimitic hyphal structure both in trama and subiculum, generative hyphae in whole basidiocarps covered by fine crystals, skeletal hyphae unchanged in KOH, not agglutinated, allantoid basidiospores measured as 3.5–4.5 × 1.0–1.2 µm, and growth on angiosperm wood. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions indicated that the new species grouped with Skeletocutis and nested in the tyromyces clade.

Transfer of selected Ahnfeltiopsis (Phyllophoraceae, Rhodophyta) species to the genus Besa and description of Schottera koreana sp. nov.

We investigated species in the family Phyllophoraceae from Korea using nuclear large-subunit ribosomal RNA, mitochondrial COI and plastid rbcL sequences and morphological examination. To understand the taxonomic relationships of Korean Ahnfeltiopsis, we also analysed topotype materials of A. leptophylla and Besa papillaeformis from California. Both individual and combined datasets revealed that Korean Ahnfeltiopsis (except A. flabelliformis) consistently formed a clade with Californian A. leptophylla and Besa papillaeformis with strong support, and this Besa clade was distinct from other genera or genetic groups in the Phyllophoraceae. The form and development of reproductive structures in topotype material of B. papillaeformis as well as those of the four Ahnfeltiopsis species supported the molecular phylogeny and underlined the distinctiveness of the Besa clade. We therefore propose to transfer four Ahnfeltiopsis species to the genus Besa as Besa catenata, B. divaricata, B. leptophylla and B. paradoxa. The concept of the genus Besa is extended to species having a heteromorphic life history and conspicuous erect gametophytes. On the basis of our molecular phylogeny, we restore A. flabelliformis to the genus Gymnogongrus. We describe a new member of the Phyllophoraceae, Schottera koreana sp. nov., a deep-water species occurring along western and southern coastlines of Korea.

Taxonomy and Phylogeny of Polyporus Group Melanopus (Polyporales, Basidiomycota) from China.

Melanopus is a morphological group of Polyporus which contains species with a black cuticle on the stipe. In this article, taxonomic and phylogenetic studies on Melanopus group were carried out on the basis of morphological characters and phylogenetic evidence of DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit nuclear ribosomal RNA gene (nSSU), the small subunit mitochondrial rRNA gene sequences (mtSSU), the translation elongation factor 1-α gene (EF1-α), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II (RPB2), and β-tubulin gene sequences (β-tubulin). The phylogenetic result confirmed that the previously so-called Melanopus group is not a monophyletic assemblage, and species in this group distribute into two distinct clades: the Picipes clade and the Squamosus clade. Four new species of Picipes are described, and nine new combinations are proposed. A key to species of Picipes is provided.

Taxonomy and multi-gene phylogeny of Haploporus (Polyporales, Basidiomycota)

Taxonomic and phylogenetic studies of Haploporus were carried out. Three species in Haploporus, H. cylindrosporus, H. septatus and H. subpapyraceus, are described as new based on morphological differences and molecular phylogenetic analyses inferred from the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit mitochondrial rRNA gene (mtSSU), the second subunit of RNA polymerase II (rpb2) and the translation elongation factor 1-α gene (TEF1) sequences. Haploporus cylindrosporus is characterized by big irregular crystals occasionally present in the subiculum, an abundant oily substance among hyphae and typically cylindrical basidiospores 10–11.5 × 4.5–5 μm; H. septatus differs from other species in the genus by its leathery to corky basidiomata when dry, small round pores (5–6 per mm), simple septate skeletal hyphae at the edge of the dissepiments, and oblong to ellipsoid basidiospores 8.5–11 × 5–6 μm; H. subpapyraceus is separated by white to cream basidiomata, numerous apically simple septate cystidioles and ellipsoid basidiospores 9–12 × 5.5–8 μm. An identification key to accepted species of Haploporus is provided.

New species and new records of Aleurodiscus s.l. (Basidiomycota) in China

Two new species from Hunan Province in central China, Acanthobasidium bambusicola and Aleurodiscus effusus, are described and illustrated. Both species have effused basidiocarps, clamped generative hyphae, acanthophyses, gloeocystidia, and amyloid, echinulate basidiospores. Acanthobasidium weirii is proposed as a new combination. In addition, Aleurodiscus ljubarskii, A. wakefieldiae, and Neoaleurodiscus fujii are reported from mainland China for the first time. Descriptions and illustrations of these three species are included. A preliminary molecular phylogenetic assessment of 11 species of Aleurodiscus sensu lato in China is presented. Phylogenetic relationships were inferred from analyses of partial DNA sequences of the nuclear large subunit ribosomal RNA (nLSU) and a combined dataset of the internal transcribed spacer (ITS) region, nLSU, and the translation elongation factor 1-α gene sequences (tef1-α).

Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera

Taxonomic and phylogenetic studies on the brown-rot fungi, Fomitopsis and its related genera, are carried out. On the basis of morphological characters and phylogenetic evidence of DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit nuclear ribosomal RNA gene (nSSU), the small subunit mitochondrial rRNA gene sequences (mtSSU), the translation elongation factor 1-α gene (tef1) and the second subunit of RNA polymerase II (rpb2), six new genera, Fragifomes, Niveoporofomes, Piptoporellus, Rhodofomitopsis, Rubellofomes and Ungulidaedalea are established. Four new species, Buglossoporus eucalypticola, Daedalea allantoidea, Piptoporellus hainanensis and P. triqueter are descibed from China. Illustrated descriptions of the novel species are provided. Identification keys to Fomitopsis and its related genera, as well as keys to the species of each genus are provided.

Two new species of Coltricia (Hymenochaetaceae, Basidiomycota) from southern China based on evidence from morphology and DNA sequence data

Two new species of Coltricia, C. austrosinensis and C. minima, are described from southern China on the basis of morphological characters and molecular evidence. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions indicated that the two new species were nested within the Coltricia clade in Hymenochaetales. Coltricia austrosinensis is characterized by centrally stipitate basidiocarps, lobed pileal margin, distinctly swollen stipe tip, cinnamon pore surface, large pores (1–3 per mm), and broadly ellipsoid basidiospores measuring 8–10 × 5.5–6.5 μm, with a distribution to date in subtropical China. Coltricia minima is characterized by tiny, centrally stipitate basidiocarps, entire pileal margin, uniform stipe, pileus bearing distinct concentric zones and pore surface dark greyish blue when fresh, small pores (3–4 per mm), narrow tramal hyphae (3.5–4 μm), and broadly ellipsoid to subglobose basidiospores measuring 6–7 × 4–5 μm, and occur in mixed tropical forests.

Phylogenetic relationship of Japanese isolates belonging to the Grosmannia piceiperda complex (Ophiostomatales)

This study was conducted to explore the morphological and phylogenetic relationships of the Japanese isolates tentatively identified as the Grosmannia piceiperda complex (Ophiostomatales, Ascomycota; asexual morph = Leptographium s.l.). The phylogenetic analyses of the internal transcribed spacer 2 and nuclear large subunit ribosomal RNA gene regions showed that the Japanese isolates belong to the G. piceiperda complex. The analyses of the partial β-tubulin and translation elongation factor-1 alpha (EF-1α) genes separated the species complex into nine and 13 lineages, respectively. Based on the β-tubulin sequences, morphologically distinct groups were included in the same clades. However, based on the EF-1α sequences, these groups could be separated into different lineages. Detailed morphological observations supported this result and confirmed that the Japanese lineages are distinct. Among the 13 recognized lineages, the Japanese isolates were separated into 11 lineages, including G. aenigmatica, G. laricis, G. piceiperda D, as well as eight lineages representing undescribed taxa.

Phylogeny and taxonomy of the genus Anomoloma (Amylocorticiales, Basidiomycota)

Anomoloma is a cosmopolitan white rot fungal genus, and it currently contains four species worldwide. In the present study, the species diversity of Anomoloma in China is investigated based on morphological characters, and relationships among the species are assessed with phylogenetic analysis based on the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (nLSU) sequences. Two new species, A. luteoalba and A. submyceliosum, are described and illustrated as well as compared with related taxa from other regions of Asia, North America and Europe. Phylogenetic analysis showed that A. luteoalba and A. submyceliosum are clearly distinct species within Anomoloma. A key to all species in this genus is provided.

Extensive genetic diversity and endemism across the global range of the oceanic copepod Pleuromamma abdominalis

Many oceanic zooplankton species have been described as cosmopolitan in distribution; however, recent molecular work has detected species complexity with highly divergent genetic lineages within several of these taxa. To further resolve the species complexity within these ecologically-important and widespread species, we performed both molecular and morphological analyses of the oceanic copepod Pleuromamma abdominalis using a comprehensive collection of material from 944 individuals collected at 46 sites across the global ocean. Phylogenetic analyses of mitochondrial cytochrome oxidase subunit I (mtCOI) sequences detected eighteen divergent evolutionary lineages within P. abdominalis, with an additional four singleton specimens that were also genetically divergent. Two phylogenetically distinct groups, PLAB1 and PLAB2, were supported by concordant sequence variation in the nuclear large subunit ribosomal RNA gene (nLSU). Within PLAB1, two mtCOI clades, 1a-1 and 1b-1 were observed, and each clade contained geographically distinct sub-clades 1a-2 and 1b-2. PLAB2 was composed of sixteen well-supported mtCOI clades (2a–2p) as well as four singletons. High genetic divergence among the mtCOI lineages within both PLAB1 and PLAB2, ranging between 9.2–11.2% and 4.3–18.9% K2P distances respectively, suggests the presence of additional species within these groups. Significant differences were observed in the presence and shape of antennule spines of adult females between sympatric clades with genetic distances greater than 5.7–7.0% (K2P). The biogeographic distributions of mtCOI clades indicated greater specialization to particular oceanographic provinces than observed in the nominal species P. abdominalis, with mtCOI clades ranging from antitropical in subtropical waters of all three ocean basins (Atlantic, Pacific and Indian; clade 1b-1 and 2a) to taxa that are endemic to a particular ocean region, for example restricted to equatorial waters of the Atlantic Ocean (clade 1b-2 and 2b). We hypothesize that many of these mtCOI clades are likely distinct, and currently undescribed species. The well-known high dominance of P. abdominalis across a range of pelagic habitats may occur as a spatial composite of genetically-distinct species with more restricted distributions and greater ecological specialization to particular marine habitats than was previously recognized.

A molecular phylogeny and classification of Anisoptera (Odonata)

A phylogeny of Anisoptera employing 510 representatives of 184 genera (of ca. 380) in 11 families is presented based on an analysis of over 10,000 nucleotides from portions of the large and small subunit nuclear and mitochondrial ribosomal RNA’s, the mitochondrial protein coding genes COI and COII, and portions of the nuclear protein coding genes EF-1α and Histone H3. Ribosomal sequences were structurally aligned and sequences carefully checked to eliminate alignment errors, contamination, misidentification and paralogous gene amplicons. Both the RAxML and Bayesian topology based on consolidation of data at the generic level is ((Austropetaliidae, Aeshnidae), ((Gomphidae, Petaluridae), ((Chlorogomphidae, (Neopetaliidae, Cordulegastridae)), (Synthemistidae, (Macromiidae, (Corduliidae, Libellulidae)))))). As the positions of Petaluridae, Chlorogomphidae, Neopetaliidae, and Cordulegastridae are weakly supported, possible alternative hypotheses are discussed. New taxonomic groups established include: in Gomphidae, Stylogomphini trib.n. and Davidioidini trib.n., and in Libellulidae, Dythemistinae subfam.n. including Dythemistini trib.n., Pachydiplactini trib.n. and Elgini trib.n. New taxonomic arrangements include: placement of Hemigomphini in Ictinogomphinae, and provisional expansion of Synthemistidae to include Gomphomacromiinae and a number of genera formerly placed in several small subfamilies of Corduliidae. Idomacromiinae is placed sister to remaining Synthemistidae s.l. based on molecular analysis of Idomacromia Karsch and Oxygastra Selys. Hemicorduliidae and Macrodiplactidae are nested well within Corduliidae and Libellulidae, respectively, and therefore are not accorded family rank. Eleven monophyletic subdivisions of Libellulidae are tentatively recognized as subfamilies: Dythemistinae subfam.n.; Sympetrinae (including Leucorrhiniini and Rhyothemistini); Macrodiplactinae; Brachydiplactinae; Tetrathemistinae; Trameinae; Zyxommatinae; Palpopleurinae; Diastatopidinae; Pantalinae (including Trithemistini and Onychothemistini); and Libellulinae. Zygonychini is paraphyletic to and therefore included within Onychothemistini.

Mycorrhizal synthesis of the edible mushroom Turbinellus floccosus with Abies religiosa from central Mexico

The ectomycorrhizal (EM) synthesis between Turbinellus floccosus with Abies religiosa was accomplished under controlled conditions by using seedlings planted in a sterilized peat moss-vermiculite substrate and cultured mycelium. Yellow to brownish EM root tips were observed 3 mo after inoculation. We identified the mycobiont of the synthesized EM through sequence similarity of the nuclear large subunit ribosomal RNA gene (LSU) between three experimental sources: basidiomata, synthesized EM root tips and inoculated cultured mycelium. The morphological and anatomical characteristics of the synthesized EM root tips were presented and described.

A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda)

Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS–LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts.

Mensularia rhododendri (Hymenochaetaceae, Basidiomycota) from southwestern China

A new species Mensularia rhododendri is described from southwestern China on the basis of both morphological characters and molecular evidence. Phylogenetic analysis based on nuclear large subunit (nLSU) ribosomal RNA gene shows that the new species belongs to Mensularia. Morphologically, the new species is mostly similar to Mensularia hastifera by sharing similar hymenial setae and basidiospores in shape and size. However, M. rhododendri differs in smaller pores (5–6 per mm), thinner fruit body (up to 2.5 mm), shorter and unbranched hyphoid setae (up to 110 µm long) present in trama only, basidiospores not collapsed, and growth on Rhododendron in nearly the timber line of southwest China, while M. hastifera has relatively larger pores (3–4 per mm), thicker fruit body (up to 10 mm), longer and sometimes branched hyphoid setae (up to 300 µm long) frequently present in both trama and dissepiments, and mostly collapsed basidiospores, and occurs mostly on Fagus in the temperate area of Central Europe. The morphological differences between M. rhododendri and other similar species of Mensularia are also compared.

High morphological plasticity and global geographical distribution of the Pacific broad tapeworm Adenocephalus pacificus (syn. Diphyllobothrium pacificum): Molecular and morphological survey

The most important causative agent of human diphyllobothriosis in South America, Diphyllobothrium pacificum, is transferred to the original genus Adenocephalus Nybelin, 1931; revised and redescribed on the basis of the evaluation of an extensive material collected mainly from northern fur seal, Callorhinus ursinus, from St. Paul Island, Alaska. Detailed analysis of morphological and morphometrical data shows a high variability in most of the characteristics traditionally used in diagnosis of diphyllobothriid tapeworms. Phylogenetic analyses based on newly characterised sequences of mitochondrial cytochrome c oxidase subunit 1 and nuclear large subunit ribosomal RNA genes consistently reveal Adenocephalus pacificus as a sister lineage to the clade formed of the remaining Diphyllobothrium species and other genera (Digramma, Diplogonoporus, Ligula). Despite the generally similar morphology, A. pacificus can be differentiated from the closely related taxa in the presence of transverse papilla-like tegumental protuberances distributed anteriorly, separated by narrow semicircular grooves on the ventral surface of proglottids between their anterior margin and the anterior edge of the male gonopore, and relatively small eggs. A. pacificus displays a relatively low host specificity (found in 9 of 16 otariids, and in accidental hosts such as man, dog and jackal, the latter representing a new host) and a uniquely wide geographical distribution on both hemispheres. In addition, suitability of morphological criteria used in diagnostics of diphyllobothriid cestodes is discussed.