LSU Analyses Research Articles

Taxonomic and Phylogenetic Placement ofPhaeodimeriella(Pseudoperisporiaceae, Pleosporales)

Abstract Phaeodimeriella is an epiphytic or pathogenic genus that occurs on plant surfaces associated with other fungi and belongs in the family Pseudoperisporiaceae (Dothideomycetes family, incertae sedis). The taxonomy of Phaeodimeriella has been problematic because of lack of molecular data and as some of the important morphological characters having not been reported. The present study clarifies the phylogenetic placement of Phaeodimeriella using fresh collections from northern Thailand. Two Phaeodimeriella species are characterized based on combined analyses of LSU, SSU, TEF and RPB2 sequence datasets. In the phylogenetic analyses, the two Phaeodimeriella species form a distinct lineage, adjacent to the Lentitheciaceae and Bambusicolaceae, in the order Pleosporales. The genus Phaeodimeriella is re-described and illustrated using modern concepts from fresh collections and provided with molecular data. The new species Phaeodimeriella cissampeli and P. dilleniae are introduced based on morphological cha...

Dictyosporiaceae fam. nov.

Dictyosporiaceae fam. nov. is introduced to accommodate a holomorphic group of Dothideomycetes that are saprobes on decaying wood and plant debris in terrestrial and freshwater habitats. The sexual morph comprises Dictyosporium meiosporum, D. sexualis, Gregarithecium curvisporum, Pseudocoleophoma calamagrostidis and P. polygonicola. The sexual morphs are characterized by immersed to erumpent, superficial, globose to subglobose, dark brown to black ascomata, bitunicate asci, and septate, hyaline, sheathed ascospores. The asexual morphs are hyphomycetous with brown, multi-septate, cheirosporous conidia, produced from holoblastic conidiogenous cells, on micronematous conidiophores. Phylogenetic analyses of LSU, SSU and TEF1 sequence data place the genera with cheirospores in a monophyletic clade in the order Pleosporales. Phylogenetic analyses based on ITS sequence data show the family to comprise 44 distinct lineages that correspond to ten genera and an undetermined genus. Four new genera Dictyocheirospora, Dictyopalmispora, Jalapriya and Vikalpa, and eight new species Dictyocheirospora bannica, D. rotunda, D. vinaya, Dictyopalmispora palmae, Dictyosporium olivaceosporum, D. sexualis, Jalapriya pulchra, and Vikalpa lignicola, are introduced in the family.

Chaetothyrina mangiferae sp. nov., a new species of Chaetothyrina

Chaetothyrina musarum and C. mangiferae sp. nov. (Micropeltidaceae, Dothideomycetes) are reported from fruits of Musa sp. (Musa acuminata × Musa balbisiana) and Mangifera indica, respectively. Introduction of a new species, Chaetothyrina mangiferae, and provision of a reference specimen for C. musarum with sequence data, supported by morphology will help to stabilize the taxonomy of the genus and family. Maximum likelihood and Bayesian analyses of LSU and SSU sequence data show that C. musarum forms a distinct clade with other genera in Micropeltidaceae within Capnodiales and C. mangiferae clusters in a poorly supported clade in Dothideomycetes, Illustrated accounts of Chaetothyrina musarum (reference specimen) and C. mangiferae are provided and compared with similar taxa. This is the first report of C. musarum causing sooty blotch and flyspeck disease on Musa sp. (Musaceae) in Thailand and C. mangiferae causing sooty blotch and flyspeck disease of Mangifera indica (Anacardiaceae) worldwide.

Phylogenetic relationships and morphological reappraisal of Melanommataceae (Pleosporales)

The family Melanommataceae is widespread in temperate and subtropical regions and species invariably occur on twigs or bark of various woody plants in terrestrial, marine or freshwater habitats. In this paper, the type species of 26 genera of the family are re-described and illustrated. A multi-gene phylogeny based on maximum likelihood and Bayesian analyses of LSU, SSU, RPB2 and EF-1 alpha sequence data of species of Melanommataceae is provided. The new genera, Muriformistrickeria, Pseudostrickeria and Thysanolaenae are introduced. Anomalemma is synonymized under Exosporiella. Acrocordiopsis, Astrosphaeriella, Beverwykella, Caryosporella, Sporidesmiella and Pseudotrichia are excluded from Melanommataceae based on molecular phylogenetic analyses. Presently, 20 genera are accepted in Melanommataceae. Based on the phylogenetic data, five new species, Byssosphaeria siamensis, Herpotrichia vaginatispora, Pseudostrickeria muriformis, Pseudostrickeria ononidis and Muriformistrickeria rubi, are introduced.

Multi-Gene Analyses Reveal Taxonomic Placement ofScolicosporium minkeviciusiiin Phaeosphaeriaceae (Pleosporales)

Scolicosporium minkeviciusii, was newly collected in Italy, and subjected to morpho-molecular analyses. Morphological characters clearly indicate that this species is a coelomycete. Combined maximum-likelihood and maximum-parsimony analyses of LSU and SSU gene sequence data of S. minkeviciusii grouped it in Phaeosphaeriaceae with Phaeosphaeria nodorum, P. oryzcie and Stagonospora foliicola, although the type species of Scolicosporium, S. macrosporium, which has not been sequenced, is considered to belong in the family Pleomassariaceae. In this study, we designate an epitype for Scolicosporium minkeviciusii. The placement of S. macrosporium and Scolicosporium sensu stricto remains uncertain and further morpho-molecular studies are necessary to confirm the taxonomic placement of this type species and to delimit this genus.

Sequence Data Reveals Phylogenetic Affinities ofAcrocalymma aquaticasp. nov.,Aquasubmersa mircensisgen. et sp. nov. andClohesyomyces aquaticus(Freshwater Coelomycetes)

Three coelomycetous ascomycetes, Acrocalymma aquatic sp. nov., Aquasubmersa mircensis gen. & sp. nov., and Clohesyomyces aquaticus are reported from northern Thailand. All taxa are characterized, illustrated and subjected to awnalyses of LSU, SSU and/or ITS rDNA gene sequence data to establish their phylogenetic placement in the ascomycetes. Acrocalymma is a monotypic genus in a distinct lineage of Pleosporales which is basal to Morosphaeriaceae as confirmed by our combined SSU and LSU analysis. Acrocalymma aquatica sp. nov., differs in morphology and gene sequence data from other species in the genus. Aquasubmersa mircensis gen. et sp. nov. is phylogenetically unrelated to any other dothideomycetous genus and is introduced as a new genus. Sequence data from Clohesyomyces aquaticus facilitated its accommodation in Lindgomycetaceae.

Phylogeny of Chaetothyriaceae in northern Thailand including three new species

In a recent study unusual taxa of epiphyllous ascomycota belonging to Chaetothyriaceae (Eurotiomycetes) were collected in northern Thailand. This family is poorly understood due to morphological confusion and lack of phylogenetic studies. This paper deals with three new species, Ceramothyrium thailandicum, Chaetothyrium brischofiacola and Phaeosaccardinula ficus, which are fully described and illustrated. A DNA sequence analyses of LSU and ITS rDNA genes shows that the new species cluster in the Chaetothyriaceae. This paper adds six sequences for Chaetothyriaceae to GenBank, providing much needed data for the family.

A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand

Trischistoma contains four accepted species. In this paper four more new species are added to the genus. Morphologically, these four new species can be briefly characterized as follows: T. triregius sp. nov. by having a pair of lateral cervical setae; T. otaika sp. nov. by having a post-vulval uterine sac and a prominent dorsal tooth; T. waiotama sp. nov. by having a single ventromedian cervical seta; T. tukorehe sp. nov. by having two prominent dorsal teeth and long body length. Molecularly, T. triregius sp. nov., T. otaika sp. nov., T. waiotama sp. nov. and one published species, T. monohystera can be differentiated by SSU & LSU analysis. Among the four previously described species, the main distinguishing feature for T. pellucidum and T. gracile is the absence of a postvulval uterine sac, which differentiates them from T. monohystera, and T. equatoriale. All previously described species also can be differentiated by: body length and values of De Man’s Indices a, b, c, c’ and V. A key is provided for all eight species of the genus.

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.

A comparative study of Neogymnomyces virgineus, a new keratinolytic species from dung, and its relationships with the Onygenales

Isolations of onygenalean fungi were made recently from different dung samples from Italy. A striking snow-white species with gymnothecial ascomata, developed in damp chamber on dormouse dung collected in a cave, was subjected to keratinolytic tests and morphological, cultural, and phylogenetic studies. The keratinolytic ability of this species, associated with a Chrysosporium anamorph and a sexual state of appendiculate reticuloperidia and oblate ascospores, allows it to be accomodated in Onygenaceae. White ascomata, blunt or subcapitate peridial appendages, pitted ascospores, and tuberculate conidia suggest it to be a new Neogymnomyces, and this was confirmed by parsimony analyses of LSU and ITS nrDNA sequences. Following recent phylogenetic analyses, the morphological and physiological features of order Onygenales and its families are re–examined and discussed. After the introduction of a new species, Neogymnomyces is reviewed and compared with all other genera in Onygenaceae. The Chrysosporium imperfect state of Neogymnomyces virgineus is described and compared to the anamorph of N. demonbreunii. It is also compared to the atypical Chrysosporium merdarium and to several other Chrysosporium species with echinulate to verrucose–tuberculate conidia, isolated from guano, dung, and nitrogen–rich soils in caves. The onygenalean fungi isolated from any kind of dung are discussed and their facultative coprophily ascribed to variable faecal contents of keratin or other degradable substances. A key to the families and genera of the Onygenales is provided.

Phylogenetic relationships of five genera of Xylariales and Rosasphaeria gen. nov. (Hypocreales)

Eight inconspicuous non-stromatic perithecial fungi immersed in plant tissue are assessed with respect to their morphology, ecology and phylogenetic position. Emphasis is laid on two genera now and then placed in the family Hyponectriaceae, Xylariales: Leiosphaerella with its type species L. praeclara occurring on Vaccinium, and Pseudomassaria with its type species P. chondrospora occurring on Tilia. In molecular phylogenetic analyses of LSU and ITS sequences, the generic types of these genera are closely related, but their familial affiliation within Xylariales remains unresolved. Pseudomassaria sepincoliformis clusters with P. chondrospora, whereas P. fallax is not congeneric with Pseudomassaria and P. lycopodina is combined in Leiosphaerella despite its apiospores. Three species thought to belong to Leiosphaerella are re-assessed: L. moravica that occurs on Rosa, is disposed in the new genus Rosasphaeria, which is close to Eucasphaeria in the Niessliaceae (Hypocreales), according to multi-gene phylogenetic analyses (ITS, LSU, rpb2 and tef1). For L. vexata the genus Pseudomassariella is revived. A Leiosphaerella-like fungus on Lycopodium is described as the new species Monographella lycopodina. In addition the phylogenetic relationships of two fungi forming superficial stromata are here clarified: Collodiscula japonica belongs to the Xylariaceae, while Melogramma campylosporum may currently be interpreted as representing a family of its own, the Melogrammataceae.

Morphological and molecular characteristics of a poorly known marine ascomycete, Manglicola guatemalensis (Jahnulales: Pezizomycotina; Dothideomycetes, Incertae sedis): new lineage of marine ascomycetes

The poorly known marine ascomycete Manglicola guatemalensis from Trang and Trat provinces, Thailand, were collected in 2005 and 2006 on the brackish water palm Nypa fruticans. This fungus is known only from two previous collections. This paper reports on the morphological characteristics and molecular phylogeny of this unique marine bitunicate ascomycete. Manglicola guatemalensis has large clavate to obtusely fusiform ascomata, wide ostioles, bitunicate asci, cylindrical, thick-walled, unequally one-septate ascospores, constricted at the septum, apical cell larger, chestnut-brown and a smaller light brown basal cell. Ascospores germinate readily, always from the basal cell. Four isolates from different locations were selected for the phylogenetic study. Regions of the rDNA gene, including SSU and LSU, were sequenced and combined. Molecular data places M. guatemalensis in the Jahnulales with high bootstrap support; all strains are monophyletic. In the combined SSU and LSU analyses the Jahnulales comprises four subclades, A, B, C and D. Subclade A comprises Jahnula species and two anamorphic fungi, Brachiosphaera tropicalis and Xylomyces chlamydosporus. In subclade B Manglicola strains form a sister group of the Aliquandostipite species Aliquandostipite crystallinus, A. khaoyaiensis, Jahnula siamensiae and Patescospora separans. Subclade C comprises Jahnula species, Jahnula aquatica, J. granulosa and J. rostrata, while Megalohypha aqua-dulces constitutes subclade D. Therefore Manglicola forms another lineage of marine fungi.

A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand

Tripylina contains six accepted species. Morphologically, five new species can be briefly characterized as follows: T. tearoha sp. nov., T. manurewa sp. nov. and T. tamaki sp. nov. each have a single ventromedian seta and two pairs of lateral setae in the cervical region; T. tearoha sp. nov. differs from T. tamaki sp. nov. by de Man’s Index a (25–30 vs 20– 23), and differs from T. manurewa sp. nov. by the distance of the ventromedian cervical seta from the head end (62–77 vs 78–86 μ m). T. manurewa sp. nov. differs from T. tamaki sp. nov. by de Man’s Index a (24–29 vs 20–23). Molecularly, these three new species can be differentiated by SSU & LSU analysis. Tripylina yeatesi sp. nov. and T. kaikoura sp. nov. are characterised by relatively long bodies, and the absence of ventromedian cervical setae; Tripylina yeatesi sp. nov. differs from T. kaikoura sp. nov. by de Man’s Indices: a (29–30 vs 22–23), b (5.8–6.0 vs 6.0–6.2), c (18–26 vs 14–16) and c’ (2.0–2.6 vs 2.7–3.0), respectively. Among the six previously described species, the main distinguishing features for T. arenicola and T. ursulae are their subventral stoma denticles lying posterior to the dorsal tooth, which differentiates them from T. longa, T. macroseta, T. sheri and T. stramenti. All published species also can be differentiated by: body length; values of De Man’s Indices a, b, c, c’ and V; presence or absence of setae and setal positions. A key is provided for all eleven species of the genus.

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.

Galerina Earle: A polyphyletic genus in the consortium of dark-spored agarics

The basidiomycete genus Galerina Earle accommodates more than 300 small brown-spored agarics worldwide, predominantly described from the Northern hemisphere. The delimitation of species and infrageneric units hitherto has been based on morphological and, to some extent, ecological characters. In this study we have analyzed nuclear ribosomal LSU and ITS sequences to reveal infrageneric phylogeny and the phylogenetic placement of Galerina among the dark-spored agarics. Sequences from 36 northern hemisphere Galerina species and 19 other dark-spored taxa were analyzed, some of them obtained from EMBL/GenBank. Our results, received from Bayesian and distance methods, strongly suggest that Galerina is a polyphyletic genus. The LSU analysis shows that Galerina is composed of three or four separate monophyletic main groups. In addition, a few species cluster together with other dark-spored agarics. The same groups are recognized in the ITS tree and they correspond roughly to previously recognized subgenera or sections in Galerina. With high support our LSU analysis suggests that Gymnopilus is a monophyletic genus and that Gymnopilus and one of the Galerina lineages (“mycenopsis”) are sister groups. The analyses further indicate that the Galerina lineages, as well as the genus Gymnopilus, could be referred to a strongly emendated family Strophariaceae, which corresponds largely to the family as circumscribed by Kühner (1980). Our results affirm that morphological characters often are highly homoplastic in the agarics. At the present stage formal taxonomic consequences or nomenclatural changes are not proposed.

Galerina Earle: A polyphyletic genus in the consortium of dark-spored agarics

The basidiomycete genus Galerina Earle accommodates more than 300 small brown-spored agarics worldwide, predominantly described from the Northern hemisphere. The delimitation of species and infrageneric units hitherto has been based on morphological and, to some extent, ecological characters. In this study we have analyzed nuclear ribosomal LSU and ITS sequences to reveal infrageneric phylogeny and the phylogenetic placement of Galerina among the dark-spored agarics. Sequences from 36 northern hemisphere Galerina species and 19 other dark-spored taxa were analyzed, some of them obtained from EMBL/GenBank. Our results, received from Bayesian and distance methods, strongly suggest that Galerina is a polyphyletic genus. The LSU analysis shows that Galerina is composed of three or four separate monophyletic main groups. In addition, a few species cluster together with other dark-spored agarics. The same groups are recognized in the ITS tree and they correspond roughly to previously recognized subgenera or sections in Galerina. With high support our LSU analysis suggests that Gymnopilus is a monophyletic genus and that Gymnopilus and one of the Galerina lineages ("mycenopsis") are sister groups. The analyses further indicate that the Galerina lineages, as well as the genus Gymnopilus, could be referred to a strongly emendated family Strophariaceae, which corresponds largely to the family as circumscribed by Kühner (1980). Our results affirm that morphological characters often are highly homoplastic in the agarics. At the present stage formal taxonomic consequences or nomenclatural changes are not proposed.

Implications of molecular characters for the phylogeny of the genus Entyloma

Many species formerly listed in Entyloma have been removed and are now placed in several orders. This study aims to clarify the framework of the genus Entyloma and the phylogeny of these plant parasitic smut fungi with molecular data. Analyses of LSU and ITS sequences are presented and support the monophyly of the order Entylomatales. The sequences show higher similarities within the examined species of Entyloma than within other smut families and genera, suggesting a recent radiation. Within the Entylomatales a cluster of anamorphic Tilletiopsis washingtonensis, T. lilacina and T. cremea collections is the sister group to Entyloma. The phylogenetic relationships in the genus Entyloma are a result of joint evolution with their hosts. The analyses of the sequence data show unresolved groups on Ranunculales and a well-supported group on Asteridae.