LSU Sequence Data Research Articles

Delonicicola siamensegen. & sp. nov. (Delonicicolaceaefam. nov., Delonicicolales ord. nov.), a Saprobic Species fromDelonix regiaSeed Pods

This paper introduces a new genus Delonicicola, to accommodate D. siamense sp. nov., which was found associated with Delonix regia seed pods, collected in Chiang Rai Province, Thailand. ITS sequence data confirmed a close relationship of Delonicicola with Liberomyces and Asteromella in Xylariomycetidae. Phylogenetic and molecular clock analyses of combined LSU, SSU and RPB2 sequence data provide evidence for a new family Delonicicolaceae and a new order Delonicicolales in Xylariomycetidae. Members of Delonicicolaceae are saprobes, endophytes or pathogens of angiosperms and it is characterized by pseudostromatal immersed, papillate ascomata, short pedicellate asci with a simple apex and 1-septate, hyaline ascospores. The asexual morph is coelomycetous with pycnidial conidiomata and allantoid, filiform or bacilloid, hyaline conidia.

The genus Phillipsia from China and Thailand

The genus Phillipsia (Sarcoscyphaceae) is characterized by large, bright-coloured, sub-stipitate apothecia, sub-operculate asci and asymmetrical ascospores with longitudinal striations. Morphological and phylogenetic studies were carried out on new collections of Phillipsia from China and Thailand. Phillipsia subpurpurea are recorded from China and Phillipsia gelatinosa from Thailand is introduced as a new species to science. Our new collections are confirmed to be divergent from other species of Phillipsia based on morphological examination and molecular phylogenetic analyses of ITS and LSU sequence data. Descriptions and figures are provided for the taxa which are also compared with allied taxa.

<span style="font-size: 10px;">Two new species of Dyfrolomyces (Dyfrolomycetaceae, Dothideomycetes) from </span><span style="font-size: 10px;">karst landforms</span>

A survey of saprobic fungi yielded two new ascomycetes, Dyfrolomyces maolanensis and D. thamplaensis, which were isolated from dead branches collected from karst landforms of China and Thailand respectively. Both of them are characterized by immersed, clypeate, papillate ascomata, long cylindrical, short-pedicellate asci and fusiform, guttulate, 3-septate ascospores. Molecular analysis of combined LSU, SSU and TEF1-a sequence data placed them in the family Dyfrolomycetaceae with good support. Morphologically, they differ from other species of Dyfrolomyces by their ascospores, which are normally 3-septate, fusiform with acute or angular ends. And those reported Dyfrolomyces species were collected aquatic habitats, while our new species in this study were collected from terrestrial habitats. Saccardoella aquatica shares the similar morphology with these two new taxa, but can be distinguished in having its smaller asci and ascospores. Therefore, we introduce D thamplaensis and D. maolanensis here as new species and also transfer S. aquatica to Dyfrolomyces based on its similar morphological characters, as well as the molecular evidence of above two new taxa.

Phylogenetic reassessment of Nigrospora: Ubiquitous endophytes, plant and human pathogens.

Species of Nigrospora commonly occur as plant pathogens, endophytes or saprobes, and have been shown to be extremely interesting for the discovery of novel metabolites. The familial placement, as well as phylogenetic relationships among Nigrospora species remain ambiguous. In this study, Nigrospora (= Khusia) is confirmed as a monophyletic genus belonging to Apiosporaceae (Xylariales), based on a phylogeny inferred from LSU sequence data. A multi-locus phylogeny based on ITS, TEF1-α and TUB2, in conjunction with morphological characters, host associations, and ecological data was employed for species delimitation in Nigrospora, as well as identification of 165 recently collected isolates from China, and three from Europe. In total 13 novelties are proposed including 12 new species and 1 new combination. Five species are re-described based on an examination of type specimens and/or fresh collections. New species described in this paper include: N. aurantiaca, N. bambusae, N. camelliae-sinensis, N. chinensis, N. guilinensis, N. hainanensis, N. lacticolonia, N. osmanthi, N. pyriformis, N. rubi, N. vesicularis and N. zimmermanii. Furthermore, N. vietnamensis is transferred to Arthrinium. Our results indicate a high level of species diversity within Nigrospora, with a general lack in host specificity. Taxa that cluster basal in Nigrospora have wide host ranges, whereas those that diverged later tend to have narrow host ranges. The currently available data suggest, therefore, that the general evolutionary direction in the genus Nigrospora is from a wide to a narrow host range.

Towards a natural classification of Annulatascaceae-like taxa: introducing Atractosporales ord. nov. and six new families

Species with relatively small, membraneous, black ascomata, with or without long necks, unitunicate, cylindrical asci with apical rings and fusiform, hyaline ascospores with or without mucilaginous sheaths are common in freshwater habitats in tropical and temperate regions. Many of these taxa have originally been recorded as Annulatascaceae-like taxa. Twenty genera have been included in the family Annulatascaceae, mostly based on morphological characters, while molecular work and phylogenetic analyses are lacking for many genera. In this study, nine new Annulatascaceae-like taxa collected from Thailand were morphologically examined. Pure cultures obtained from single ascospores were used in molecular studies. The nine new strains and several other strains of Annulatascaceae-like Sordariomycetes species were used to establish phylogenetic and evolution relationships among the taxa, based on combined LSU, SSU, ITS and RPB2 sequence data. Phylogenetic analyses provide evidence to introduce one new order and six new families, to accommodate taxa excluded from Annulatascaceae sensu stricto. A new order Atractosporales is established based on the molecular study, including three new introduced families Conlariaceae, Pseudoproboscisporaceae and Atractosporaceae. Conlariaceae is introduced for the genus Conlarium which comprises two species, Conlarium duplumascosporun and a new Hyphomycetous asexual morph taxon Conlarium aquaticum which has subglobose or irregular, brown, clathrate, muriform conidia. Pseudoproboscisporaceae includes Pseudoproboscispora and Diluviicola, while Atractosporaceae includes the genera Rubellisphaeria and Atractospora. Barbatosphaeria, Xylomelasma and Ceratostomella form a distinct stable lineage which is introduced as a new family Barbatosphaeriaceae in Diaporthomycetidae families incertae sedis. A new family Lentomitellaceae is introduced in Diaporthomycetidae families incertae sedis, to accommodate the genus Lentomitella. Woswasiaceae is introduced to accommodate Woswasia, Xylochrysis and Cyanoannulus in Diaporthomycetidae families incertae sedis. Three new species of Fluminicola viz. F. saprophytica, F. thailandensis and F. aquatica are introduced. A new sexual morph, Dictyosporella thailandensis, is reported and Dictyosporella is excluded from Annulatascaceae and placed in Diaporthomycetidae genera incertae sedis. The first sexual morph of Sporidesmium, S. thailandense is also described. The new species Atractospora thailandensis, Diluviicola aquatica and Pseudoproboscispora thailandensis are also introduced. Platytrachelon is added to Papulosaceae based on phylogenetic analysis and morphological characters. Aquaticola, Fusoidispora and Pseudoannulatascus are excluded from Annulatascaceae and placed in Diaporthomycetidae genera incertae sedis. Mirannulata is accommodated in Sordariomycetes, genera incertae sedis.

Phylogenetic revision of Camarosporium (Pleosporineae, Dothideomycetes) and allied genera.

A concatenated dataset of LSU, SSU, ITS and tef1 DNA sequence data was analysed to investigate the taxonomic position and phylogenetic relationships of the genus Camarosporium in Pleosporineae (Dothideomycetes). Newly generated sequences from camarosporium-like taxa collected from Europe (Italy) and Russia form a well-supported monophyletic clade within Pleosporineae. A new genus Camarosporidiella and a new family Camarosporidiellaceae are established to accommodate these taxa. Four new species, Neocamarosporium korfii, N. lamiacearum, N. salicorniicola and N. salsolae, constitute a strongly supported clade with several known taxa for which the new family, Neocamarosporiaceae, is introduced. The genus Staurosphaeria based on S. lycii is resurrected and epitypified, and shown to accommodate the recently introduced genus Hazslinszkyomyces in Coniothyriaceae with significant statistical support. Camarosporium quaternatum, the type species of Camarosporium and Camarosporomyces flavigena cluster together in a monophyletic clade with significant statistical support and sister to the Leptosphaeriaceae. To better resolve interfamilial/intergeneric level relationships and improve taxonomic understanding within Pleosporineae, we validate Camarosporiaceae to accommodate Camarosporium and Camarosporomyces. The latter taxa along with other species are described in this study.

NovelNeoacanthostigmaSpecies from Aquatic Habitats

Helicosporous hyphomycetes are a morphologically fascinating group of Tubeufiales. Ten dematiaceous helicosporous asexual morphs and two sexual morphs collected from aquatic habitats are characterized in this study using morphological features and phylogenetic analyses. Four new species of Neoacanthostigma, viz. N. aquaticum, N. brunneisporum, N. guangxiense and N. latisporum, are described and illustrated. The phylogenetic analyses of combined ITS, LSU and TEF1α sequence data place all taxa in the genus Neoacanthostigma (Tubeufiaceae, Tubeufiales) and provide evidence to support the establishment of the new taxa. The differentiating morphological characters of Neoacanthostigma with other helicosporous species are compared and discussed. A key to all Neoacanthostigma species is also provided.

Study in Agaricus subgenus Minores and allied clades reveals a new American subgenus and contrasting phylogenetic patterns in Europe and Greater Mekong Subregion

Within Agaricus subg. Minores, A. sect. Minores remains a little-studied section due generally to its delicate sporocarps often lacking taxonomically relevant morphological characters. To reconstruct the section, using the recent taxonomic system based on divergence times, and to evaluate the species diversity of A. sect. Minores in the Greater Mekong Subregion, 165 specimens were incorporated in phylogenetic analyses. A dated tree based on nuclear ITS, LSU and tef1-α sequence data allowed us to better circumscribe A. subg. Minores and to propose a new subgenus, A. subg. Minoriopsis, which is only known from tropical and subtropical regions of the Americas. A larger tree based on ITS sequences indicated that, with 81 phylogenetic species, the reconstructed section Minores is now one of the largest sections in the genus. Within A. subg. Minores, a new section, A. sect. Leucocarpi, and eleven new species are described from the Greater Mekong Subregion. Thirty-eight species of A. sect. Minores from this region of Asia were distributed in multiple clades that successively diverged over the past 24 million years. In contrast, species reported from Europe mostly grouped in a single non-tropical clade, suggesting a major species diversification following the middle Miocene climatic optimum.

Calcarisporium xylariicola sp. nov. and introduction of Calcarisporiaceae fam. nov. in Hypocreales

During a survey of fungicolous fungi, a novel taxon from the surface of stroma of an unidentified Xylaria species was collected. Phylogenetic analyses showed that this taxon clustered with Calcarisporium sp. and C. arbuscula isolates, but was resolved as a distinct species. A detailed morphological examination coupled with phylogenetic analysis indicated that the taxon represented a new species. Calcarisporium xylariicola sp. nov. is thus introduced. The new taxon is characterized by short conidiophores with swollen bases and less length/width ratio of conidia that distinguish it from other Calcarisporium species. Calcarisporium is presently placed in Hypocreales genera, incertae sedis genus. Species in the genus are largely fungicolous, or occasionally caulicolous or foliicolous, and have hyaline, erect, verticillate conidiophores and sympodial, polyblastic conidiation. A phylogenetic analysis of combined SSU, ITS, LSU, TEF and RPB2 sequence data from Calcarisporium species and other taxa in Hypocreales indicate that Calcarisporium is a distinct lineage from other families. Therefore, a new family, Calcarisporiaceae, in Hypocreales is introduced.

Four new species of Tubeufia (Tubeufiaceae, Tubeufiales) from Thailand

Tubeufia was named for a sexual morph taxon. However, several asexual morph species have been accommodated in this genus as well. In our study, four new species of Tubeufia, viz. T. filiformis, T. latispora, T. laxispora and T. mackenziei, are described and illustrated. The phylogenetic placement of the new species is confirmed by analysis of combined ITS, LSU and TEF1α sequence data. A key to Tubeufia species is provided and the new species are compared with similar fungal taxa.

Molecular Phylogeny and Morphological Characterization of Asexual Fungi (Tubeufiaceae) from Freshwater Habitats in Yunnan, China

The diversity of lignicolous freshwater fungi along a north-south latitudinal gradient are currently being studied in Asia. In this paper, we report on 18 collections of asexual morphs of Tubeufiaceae from submerged wood in rivers, streams and a lake in Yunnan Province, China. Taxa are characterized based on morphological characters and analyses of ITS, LSU and TEF1α sequence data. The new genera, Muripulchra with a single species, M. aquatica and Neohelicomyces with three new taxa (N. aquaticus, N. grandisporus, N. submersus) are introduced. Muripulchra is characterized by micronematous conidiophores and obpyriform, septate to muriform conidia. Neohelicomyces is characterized macronematous conidiophores and multi-septate, helicoid conidia. Tubeufia aquatica is introduced as a new species and its phylogenetic relationships with other taxa is discussed. The phylogenetic analyses of a concatenated ITS, LSU and TEF1α dataset place all collections in the family Tubeufiaceae (Tubeufiales) and provide evidence to support the establishment of our new taxa. The asexual morph of Tubeufia cylindrothecia, the type species of Helicomyces (H. roseus) are described herein, phylogenetic relationships assessed and reference specimens are given for these two species. Descriptions and illustrations for the new genera and species are provided with notes on their taxonomy and phylogeny.

Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes).

Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë-host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë. Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma. A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.

Pyrenochaetopsis tabarestanensis (Cucurbitariaceae, Pleosporales), a new species isolated from rice farms in north Iran

A pyrenochaeta-like species was isolated from soil in rice farms in Mazandaran Province (formerly Tabarestan), Iran. Phylogenetic analyses of SSU, LSU, ITS, β-tubulin and actin sequence data showed that the new collection clustered with species in Pyrenochaetopsis sensu stricto. In morphology, phylogeny and physiological characters, the new strains are distinct from other species, thus, they are introduced as a new species viz. P. tabarestanensis. Illustrations, descriptions and taxonomic notes are provided for P. tabarestanensis. Additionally, the phylogenetic relationships of Pyrenochaeta and Pyrenochaetopsis species in Cucurbitariaceae is discussed.

Monochaetia ilexae sp. nov. (Pestalotiopsidaceae) from Yunnan Province in China

Monochaetia is a pestalotiopsis-like genus characterized by 3–5-septate hyaline to brown conidia with single apical and basal appendages. Monochaetia species exhibit diverse conidial morphology, but many species lack molecular data and thus it is not clear if the genus is monophyletic. In this paper, combined LSU and ITS sequence data and morphological traits are used to introduce a new Monochaetia species, M. ilexae from Yunnan Province, China from dead leaves of Ilex species. Monochaetia ilexae shares similar morphology with the type, M. monochaeta and M. kansensis having fusiform conidia and has a similar range of conidia. However M. ilexae differs from M. monochaeta and M. kansensis having different conidia length, apical and basal appendage lengths. Phylogeny agrees with morphological differences allowing Monochaetia ilexae as a new species that clusters with Monochaetia species, but is separated from the main clade with high support.

A new species of Chaetothyrina on branches of mango, and introducing Phaeothecoidiellaceae fam. nov.

The new family Phaeothecoidiellaceae, introduced in this paper, comprises several species which cause sooty blotch and flyspeck diseases of several economic fruits. This results in quality issues with fruits and plants, due to the black thallus and small black dots coating the surface. Most species of Phaeothecoidiellaceae are biotrophs and are unculturable without the host material, and direct-sequencing is difficult because of the very small and flattened thyriothecia. Therefore, this fungal group is relative poorly known due to limited sampling and few in-depth studies. Microthyriales-like taxa appearing as small black dots on the surface of mango trees were collected in northern Thailand. Taxa were studied based on morphological characters and molecular analyses. Maximum likelihood and Bayesian analyses of combined ITS, LSU and SSU sequence data, indicated that the collection from branches of mango is a previously undescribed species. The new species, Chaetothyrina guttulata, is introduced in this paper with descriptions and illustrations.

Taxonomy and phylogeny of Sparticola muriformis sp. nov. on decaying grass

Members of Sporormiaceae are saprobes on plant debris, wood, soil and dung and are sometimes endophytes. In this study, a saprobic species was collected from decaying grass in China. Maximum-parsimony, maximum-likelihood and Bayesian Inference analyses of combined ITS, LSU, SSU, TEF1-alpha and RPB2 sequence data clarified the phylogenetic affinity in Sparticola. The isolate was confirmed as a new species based on morphological and phylogenetic analyses. Sparticola muriformis sp. nov. is distinguished from other taxa in Sporormiaceae by having muriform ascospores.

Establishment of Zygosporiaceae fam. nov. (Xylariales, Sordariomycetes) based on rDNA sequence data to accommodate Zygosporium

Zygosporium species are widespread on hosts and usually associated with monocotyledonous plants including Arecaceae (palms) and Pandanaceae. Zygosporium forms colonies as darkened spots on the host surface. This study recovers two Zygosporium species from China and Thailand and makes an attempt to clarify the systematic placement of Zygosporium based on morphological characteristics and phylogenetic analyses based on rDNA sequence data. Phylogenetic analyses of a combined LSU and ITS sequence data generated under Maximum Likelihood and Bayesian criteria indicate that Zygosporium species form a strongly supported monophyletic lineage basal to the Coniocessiaceae and not to the Microdochiaceae as previously assumed. Given the distinct morphological features of Zygosporium and its strongly supported monophyletic nature, a new family, Zygosporiaceae is introduced within the Xylariales.

Anthostomelloides krabiensis gen. et sp. nov. (Xylariaceae) from Pandanus odorifer (Pandanaceae)

An Anthostomella-like taxon was obtained from Pandanus odorifer (Forssk.) Kuntze (Pandanaceae) collected in Krabi Province in Thailand. Morphological data plus phylogenetic analyses of combined ITS, LSU, RPB2, and β-tubulin sequence data clearly separate this Anthostomella-like taxon from other known genera in Xylariaceae. In this paper, we introduce this taxon as a new genus, Anthostomelloides, in the family Xylariaceae, with A. krabiensis as the type. A detailed morphological description, phylogenetic tree, photomicrographs of A. krabiensis, keys to Anthostomella-like genera, and a comparison of A. krabiensis with the morphologically similar taxa in Xylariaceae are provided.

Two new species in Fuscosporellaceae from freshwater habitats in Thailand

A survey of freshwater fungi in Thailand resulted in the discovery of two new species in Fuscosporellaceae, herein described as Fuscosporella aquatica and Mucispora phangngaensis. Fuscosporella aquatica has sporodochial colonies, irregular ellipsoidal and dark brown conidia with vesicular conidiogenous cells. Mucispora phangngaensis has macronematous, solitary conidiophores with percurrent proliferations and dark brown obovoid conidia. Phylogenetic analysis based on combined LSU and ITS sequence data support their placement in Fuscosporella and Mucispora (Fuscosporellaceae, Fuscosporellales). Both species formed distinct clades from their type species and present as the second species in each genus. Descriptions and illustrations of the new taxa are provided. DNA sequence data of Parafuscosporella mucosa (from ex-type strain) are provided in this study, and confirmed its phylogenetic placement.

New species of Sporoschisma (Chaetosphaeriaceae) from aquatic habitats in Thailand

Collections of submerged wood in streams in Prachuap Khiri Khan Province, Thailand yielded three sporoschisma-like taxa. Morphological examination and phylogenetic analysis of LSU sequence data support the separation of two isolates as new species (S. palauense and S. longicatenatum) and the other as collection of S. hemipsila. The sexual morph (Melanochaeta) is again linked to the asexual genus Sporoschisma by molecular data. The new species are introduced with descriptions and illustrations and compared with the most similar species.