LSU Sequence Data Research Articles

Freshwater ascomycetes: two new species of Lindgomyces (Lindgomycetaceae, Pleosporales, Dothideomycetes) from Japan and USA

During independent surveys of freshwater ascomycetes in Japan and USA two new species of Lindgomyces were collected from submerged wood in freshwater. These species are described and illustrated based on morphological data and phylogenetic relationships based on analyses of nuclear ribosomal sequence data (partial SSU and LSU, and ITS). Lindgomyces apiculatus, collected in Japan, is characterized by immersed to erumpent, globose to subglobose ascomata; fissitunicate, cylindrical to clavate asci; and fusiform, one-septate ascospores with acute ends and short terminal appendages. Lindgomyces lemonweirensis, collected in Wisconsin, USA, differs from L. apiculatus in having clavate to cymbiform asci and oblong to fusiform ascospores that are distinctively multiguttulate and surrounded by an oval, ephemeral gelatinous sheath. The new species formed a strongly supported clade within the family Lindgomycetaceae (Pleosporales, Dothideomycetes) based on analyses of combined SSU and LSU sequence data. In addition phylogenetic analyses with ITS sequence data support the establishment of the new taxa as separate species within Lindgomyces because they were separated from each other and other Lindgomyces species based on maximum likelihood bootstrap and Bayesian analyses.

Phylogenetic relationships and reclassification of Spirosphaera lignicola, an enigmatic aeroaquatic fungus

The enigmatic Spirosphaera lignicola is revised based on recent collections from Austria. The taxon does not fit the generic circumscription of the genus Spirosphaera in its morphological features but clearly belongs to Dendroclathra. Nuclear ITS rDNA sequence data from recent collections and the type specimens indicate conspecificity of S. lignicola with Dendroclathra caeruleofusca. Spirosphaera lignicola is transferred to the genus Dendroclathra, and a recent collection with an ITS sequence identical to the type specimen is designated as epitype. Morphology is illustrated with SEM and LM pictures. Phylogenetic analyses of LSU, ITS and tef1 sequence data reveal a phylogenetic affinity of Dendroclathra to the Microascales (Hypocreomycetidae), being therefore phylogenetically distant from Spirosphaera floriformis, the generic type, which belongs to the Leotiomycetes. The recent collections are the first records of this species for Austria. The distribution and aeroaquatic ecology of D. lignicola are briefly discussed.

Asterotexis cucurbitacearum, a poorly known pathogen of Cucurbitaceae new to Costa Rica, Grenada and Panama

A pathogenic bitunicate ascomycetous fungus, identified as Asterotexis cucurbitacearum, was found repeatedly on living leaves of Cucurbita pepo (gourd) and Sechium edule (chayote) in Panama. A. cucurbitacearum represents a new report for Panama and S. edule is a new host plant for this fungus. Based on an examination of herbarium specimens, this species is also reported for the first time from Costa Rica and Grenada. Cells of the scutellum extending to the base of the fruiting structure and producing an appressorium on the leaf surface are documented for the first time. As shown by LSU sequence data, A. cucurbitacearum represents a divergent, hitherto molecularly unsampled, phylogenetic clade of the Dothideomycetes. The closest relatives, for which sequence data are available, are members of the Pleosporomycetidae and Dothideomycetes incertae sedis with sequence similarity below 90%, as shown by BLAST search. A preliminary neighbour-joining analysis indicates that A. cucurbitacearum probably belongs to the Dothideomycetidae (incertae sedis).

Description of Schistonchus microcarpus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus microcarpa in China

AbstractSchistonchus microcarpus n. sp. was recovered from the syconia of Ficus microcarpa from Shenzhen and Guangzhou, Guangdong Province, China, during a survey of nematode biodiversity from 2007 to 2009. It is characterised by possessing the combined characters of a short post-uterine sac (PUS) (3-11 μm or <0.4 vulval body diam. (VBD) long), excretory pore located just posterior to the head but anterior to the conus level of the stylet, prominent amphids, three pairs of subventral papillae on the male tail (one pair adcloacal, one pair halfway between cloaca and tail terminus, and one pair near tail tip), unique recurved and sickleshaped spicules with finely rounded tip with cucullus, amoeboid sperm, and rounded male tail tip with or without mucron. Schistonchus microcarpus n. sp. is morphologically differentiated from all other described species in this genus by the possession of a spicule with a cucullus on the tip. Schistonchus microcarpus n. sp. was easily differentiated from other sequenced species by the partial small subunit rRNA gene (SSU) and D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with partial SSU sequences suggests that S. microcarpus n. sp. is in a highly supported monophyletic clade with sequenced Schistonchus species except for S. hirtus. Based upon inferences using D3 LSU sequence data, it forms a clade with an undescribed species of Schistonchus ex F. benjamini from Australia and is part of a larger clade of Schistonchus that mostly share the character of an anteriorly placed excretory pore. Sequences of partial mtDNA COI (590 bp) from males of S. microcarpus n. sp. with and without a mucronate tail tip were identical, proving that these two morphotypes are conspecific.

Erythricium atropatanum sp. nov. (Corticiales) from Iran, based on morphological and molecular data

A new corticioid species with a pinkish fruiting body is described from East Azerbaijan Province, Iran, based on nuclear ITS and LSU sequence data and morphology. Erythricium atropatanum sp. nov. is recognized by its closely adnate, pinkish fruiting body, large and broadly ellipsoid to fusoid basidiospores with densely granulate contents, and lack of clamps. The species is nested in Corticiales and the grounds for its generic designation are discussed. A key to the known species of Erythricium is presented.

Occurrence and diversity of basidiomycetous endophytes from the oil palm, Elaeis guineensis in Thailand

Fungal endophytes associated with the oil palm, Elaeis guineensis, at an oil palm plantation in Trang Province, Thailand were investigated. Two samplings at the same site yielded 162 and 178 morphotypes. The overall colonization rate was 81 and 87%, respectively, with non-sporulating species being most common. Twenty strains were identified as basidiomycetes using morphological characteristics and confirmed at the molecular level using ribosomal DNA, LSU and ITS sequence data. Species included Fomitopsis cf. meliae, F. cf. ostreiformis, F. cf. pinicola, Perenniporia sp., Pycnoporus sanguineus, Trametes lactinea, and Schizophyllum commune. Leaves supported the greatest number of basidiomycetous taxa (11 strains) with five and four taxa from petioles and rachides, respectively. Twelve taxa produced poroid basidiomes in PDA culture, while the remainder had clamp-connections. Basidiomycetes occurring as saprobes on oil palm were also recorded and compared with those present as endophytes.

Schistonchus hirtus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus hirta in China

Abstract A nematode recovered from syconia of Ficus hirta from Guangzhou, P. R. China, during a survey of nematode biodiversity from 2007 to 2009, is described herein as Schistonchus hirtus n. sp. and is differentiated by a combination of morphological characters, including excretory pore (EP) located near the metacorpus, a short post-uterine sac (PUS) (0.5 vulval body diam. (VBD) long), rose thorn-shaped spicules, amoeboid sperm, absence of gubernaculum, three pairs of subventral papillae on the male tail, host-Ficus and host-wasp species and DNA sequence data. Morphologically, S. hirtus n. sp. is close to S. centerae, S. altermacrophylla, S. aureus, S. laevigatus and S. virens based upon the length of the PUS (about 0.5 VBD long). However, the relative position of the EP in S. hirtus n. sp. is very different from these species (near metacorpus vs near head). With regard to the EP character, S. hirtus n. sp. is very similar to S. macrophylla, S. guangzhouensis and S. caprifici where the EP is at metacorpus level. However, S. hirtus n. sp. differs from S. macrophylla and S. guangzhouensis by possessing a shorter PUS and smaller spicules, and differs from S. caprifici by a shorter female stylet and smaller spicules. Schistonchus hirtus n. sp. was easily differentiated from other sequenced species by the proportion of parsimony informative changes in the partial small subunit rRNA gene (SSU) and D2/D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with SSU sequences suggests that S. hirtus n. sp. is in a highly supported monophyletic clade with Aphelenchoides and Laimaphelenchus and is polyphyletic to other sequenced Schistonchus species. With LSU sequence data, it forms a clade with S. caprifici and they appear polyphyletic relative to S. guangzhouensis, S. centerae, S. aureus, S. laevigatus and S. virens.

Taxonomy and evolutionary relationships within species of section <I>Rimosae</I> (<I>Inocybe</I>) based on ITS, LSU and mtSSU sequence data

The present study aimed at elucidating the structure of Inocybe subg. Inosperma sect. Rimosae but included also representatives from subg. Mallocybe and the genus Auritella. Phylogenetic relationships were inferred using ITS, LSU and mtSSU sequence data. The analyses recovered the ingroup as a monophyletic, strongly supported clade. The results indicate that recognizing Auritella on the genus level renders Inocybe paraphyletic. The species traditionally placed in sect. Rimosae were found to be distributed over two strongly supported clades, Maculata and Rimosae s.s. The Maculata clade clusters with sect. Cervicolores and the two represent subg. Inosperma in a strict sense. Rimosae s.s. emerges as an independent, supported clade well separated from Inosperma s.s. Twenty-one terminal groups were correlated with morphologically distinct species. In addition several taxa on single branches and minor less supported clades were recovered. A key to the identified species of the Maculata and Rimosae s.s. clades which occur in Northwest Europe is provided.

A re-evaluation of genus Chaetomidium based on molecular and morphological characters

Chaetomidium, a genus in the Chaetomiaceae, comprises 12 species that produce similar cleistothecial ascomata with a membranous, mostly pilose, peridium. Approximately six species of this genus produce some type of modified peridium composed of cephalothecoid plates that previous authors have hypothesized to be a homologous character within the genus. To better understand the phylogenetic affiliations of Chaetomidium and distribution of the cephalothecoid peridium within this genus we performed phylogenetic analyses with LSU, β-tubulin and rpb2 sequence data. The results of these analyses showed that Chaetomidium is polyphyletic and should be restricted to its type, C. fimeti, and C. subfimeti. The remaining cephalothecoid and non-cephalothecoid species were scattered throughout the Chaetomiaceae and Lasiosphaeriaceae. The cephalothecoid species of Chaetomidium were distributed in three unrelated clades, suggesting that the morphological similarity among these particular species resulted from convergence instead of ancestry.

Phylogeny and character evolution of the coprinoid mushroom genus Parasola as inferred from LSU and ITS nrDNA sequence data.

Phylogenetic relationships, species concepts and morphological evolution of the coprinoid mushroom genus Parasola were studied. A combined dataset of nuclear ribosomal ITS and LSU sequences was used to infer phylogenetic relationships of Parasola species and several outgroup taxa. Clades recovered in the phylogenetic analyses corresponded well to morphologically discernable species, although in the case of P. leiocephala, P. lilatincta and P. plicatilis amended concepts proved necessary. Parasola galericuliformis and P. hemerobia are shown to be synonymous with P. leiocephala and P. plicatilis, respectively. By mapping morphological characters on the phylogeny, it is shown that the emergence of deliquescent Parasola taxa was accompanied by the development of pleurocystidia, brachybasidia and a plicate pileus. Spore shape and the position of the germ pore on the spores showed definite evolutionary trends within the group: from ellipsoid the former becomes more voluminous and heart-shaped, the latter evolves from central to eccentric in taxa referred to as 'crown' Parasola species. The results are discussed and compared to other Coprinus s.l. and Psathyrella taxa. Homoplasy and phylogenetic significance of various morphological characters, as well as indels in ITS and LSU sequences, are also evaluated.

Chorioactidaceae: a new family in the Pezizales ( Ascomycota) with four genera

Molecular phylogenetic and comparative morphological studies provide evidence for the recognition of a new family, Chorioactidaceae, in the Pezizales. Four genera are placed in the family: Chorioactis, Desmazierella, Neournula, and Wolfina. Based on parsimony, likelihood, and Bayesian analyses of LSU, SSU, and RPB2 sequence data, Chorioactidaceae represents a sister clade to the Sarcosomataceae, to which some of these taxa were previously referred. Morphologically these genera are similar in pigmentation, excipular construction, and asci, which mostly have terminal opercula and rounded, sometimes forked, bases without croziers. Ascospores have cyanophilic walls or cyanophilic surface ornamentation in the form of ridges or warts. So far as is known the ascospores and the cells of the paraphyses of all species are multinucleate. The six species recognized in these four genera all have limited geographical distributions in the northern hemisphere.

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.

Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera

The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloës (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also polyphyletic. Thysanorea is introduced to accommodate Periconiella papuana (Herpotrichiellaceae), which is unrelated to the type species, P. velutina (Mycosphaerellaceae).

Phylogeny of the Quambalariaceae fam. nov., including important Eucalyptus pathogens in South Africa and Australia

The genus Quambalaria consists of plant-pathogenic fungi causing disease on leaves and shoots of species of Eucalyptus and its close relative, Corymbia. The phylogenetic relationship of Quambalaria spp., previously classified in genera such as Sporothrix and Ramularia, has never been addressed. It has, however, been suggested that they belong to the basidiomycete orders Exobasidiales or Ustilaginales. The aim of this study was thus to consider the ordinal relationships of Q. eucalypti and Q. pitereka using ribosomal LSU sequences. Sequence data from the ITS nrDNA were used to determine the phylogenetic relationship of the two Quambalaria species together with Fugomyces (= Cerinosterus) cyanescens. In addition to sequence data, the ultrastructure of the septal pores of the species in question was compared. From the LSU sequence data it was concluded that Quambalaria spp. and F. cyanescens form a monophyletic clade in the Microstromatales, an order of the Ustilaginomycetes. Sequences from the ITS region confirmed that Q. pitereka and Q. eucalypti are distinct species. The ex-type isolate of F. cyanescens, together with another isolate from Eucalyptus in Australia, constitute a third species of Quambalaria, Q. cyanescens (de Hoog & G.A. de Vries) Z.W. de Beer, Begerow & R. Bauer comb. nov. Transmission electron-microscopic studies of the septal pores confirm that all three Quambalaria spp. have dolipores with swollen lips, which differ from other members of the Microstromatales (i.e. the Microstromataceae and Volvocisporiaceae) that have simple pores with more or less rounded pore lips. Based on their unique ultrastructural features and the monophyly of the three Quambalaria spp. in the Microstromatales, a new family, Quambalariaceae Z.W. de Beer, Begerow & R. Bauer fam. nov., is described.

Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota)

Research on the molecular systematics of Cortinarius, a species-rich mushroom genus with nearly global distribution, is just beginning. The present study explores infrageneric relationships using rDNA ITS and LSU sequence data. One large dataset of 132 rDNA ITS sequences and one combined da-taset with 54 rDNA ITS and LSU sequences were generated. Hebeloma was used as outgroup. Bayesian analyses and maximum-likelihood (ML) analyses were carried out. Bayesian phylogenetic inference performed equally well or better than ML, especially in large datasets. The phylogenetic analysis of the combined dataset with species representing all currently recognized subgenera recovered seven well-supported clades (Bayesian posterior probabilities BPP > 90%). These major clades are: /Myxacium s.l., /subg. Cortinarius, the /phlegmacioid clade (including the subclades /Phlegmacium and /Delibuti), the /calochroid clade (/Calochroi, /Ochroleuci and /Allutus), the /telamonioid clade (/Telamonia, /Orellani, /Anomali), /Dermocybe s.l. and /Myxotelamonia. Our results show that Cortinarius consists of many lineages, but the relationships among these clades could not be elucidated. On one hand, the low divergence in rDNA sequences can be held responsible for this; on the other hand, taxon sampling is problematic in Cortinarius phylogeny. Because of the incredibly high diversity (~2000 Cortinarius species), our sampling included <5% of the known species. By choosing type species of subgenera and sections, our sampling is strongly biased toward Northern Hemisphere taxa. More extensive taxon sampling, especially of species from the Southern Hemisphere, is essential to resolve the phylogeny of this important genus of ectomycorrhizal fungi.

Toward a Better Understanding of the Infrageneric Relationships in Cortinarius (Agaricales, Basidiomycota)

Research on the molecular systematics of Cortinarius, a species-rich mushroom genus with nearly global distribution, is just beginning. The present study explores infrageneric relationships using rDNA ITS and LSU sequence data. One large dataset of 132 rDNA ITS sequences and one combined da-taset with 54 rDNA ITS and LSU sequences were generated. Hebeloma was used as outgroup. Bayesian analyses and maximum-likelihood (ML) analyses were carried out. Bayesian phylogenetic inference performed equally well or better than ML, especially in large datasets. The phylogenetic analysis of the combined dataset with species representing all currently recognized subgenera recovered seven well-supported clades (Bayesian posterior probabilities BPP > 90%). These major clades are: /Myxacium s.l., /subg. Cortinarius, the /phlegmacioid clade (including the subclades /Phlegmacium and /Delibuti), the /calochroid clade (/Calochroi, /Ochroleuci and /Allutus), the /telamonioid clade (/Telamonia, /Orellani, /Anomali), /Dermocybe s.l. and /Myxotelamonia. Our results show that Cortinarius consists of many lineages, but the relationships among these clades could not be elucidated. On one hand, the low divergence in rDNA sequences can be held responsible for this; on the other hand, taxon sampling is problematic in Cortinarius phylogeny. Because of the incredibly high diversity (~2000 Cortinarius species), our sampling included <5% of the known species. By choosing type species of subgenera and sections, our sampling is strongly biased toward Northern Hemisphere taxa. More extensive taxon sampling, especially of species from the Southern Hemisphere, is essential to resolve the phylogeny of this important genus of ectomycorrhizal fungi.

Genera in the family Agaricaceae: evidence from nrITS and nrLSU sequences

The circumscription of the family Agaricaceae, its genera and their characters are investigated. Analyses of the ITS and LSU sequence data, separately and in combination result in exclusions and reorganization. Notholepiota areolata, a secotioid species from New Zealand, Cystoagaricus with brown, irregular-knobby spores, and Leucopholiota with gelatinized hymenophoral trama and amyloid spores, fall outside the family Agaricaceae. In the reorganization, long accepted tribe and genus definitions are amended, viz.: (1) Macrolepiota and Chlorophyllum separately are monophyletic, but not together; (2) Leucoagaricus and Leucocoprinus together form one large monophyletic clade, that also includes polyphyletic Sericeomyces; (3) Lepiota, Cystolepiota and Melanophyllum together form a monophyletic clade; (4) Secotiation has happened within several clades (e.g. Agaricus and Chlorophyllum), though not in the Leucoagaricus/Leucocoprinus clade, nor in the lineage of Macrolepiota proper; gasteroid and most secotioid species in the course of adaptation acquire coloured spores; and (5) the monovelangiocarpic Chamaemyces fracidus appears to be basal to the family and provides clues to the morphology of the ancestral Agaricaceae. Trama and developmental characters characterize the different clades, whereas spore characters play a minor role.

Characteristics and utility of nuclear‐encoded large‐subunit ribosomal gene sequences in phylogenetic studies of red algae

SUMMARYPrimer sequences are described for amplifying and sequencing a large fragment (approximately 2500 b.p.) of the nuclear‐encoded large‐subunit ribosomal RNA gene (LSU) from red algae. In comparison to RuBisCo large‐subunit gene (rbcL) and nuclear‐encoded small‐subunit ribosomal RNA gene (SSU) sequence data, LSU sequence data was intermediate in the number of phylogenetically informative positions and sequence divergence. Parsimony analysis of LSU sequences for 16 Gelidiales species resolved some nodes unresolved in rbcL and SSU parsimony trees. An analysis of LSU sequences from 13 species of red algae classified in 11 orders suggests that this gene may be useful in studies of higher‐level relationships of red algae.

A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)

Phylogenetic relationships of higher taxa of echinoids have been investigated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete SSU rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and SSU sequence data generate topologies that are not significantly in conflict (under Templeton's test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A 'total evidence' approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris, our total evidence tree suggested relationships of higher taxa as follows: Cidaroida (Phormosomatidae (Echinothuriidae (Diadematidae ((Spatangoida (Clypeasteroida, Cassiduloida)) ((Calycina, Arbacioida) (Stomopneustidae (Glyphocidaridae (Temnopleuridae (Echinometridae (Echinidae, Stronglyocentridae)))))))))). Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.