Nuclear Ribosomal LSU Research Articles

Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential.

Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.

<p><strong><em>Phaeoclavulina liliputiana sp. nov. </em></strong><strong>(Gomphaceae, Gomphales) a new endemic species from Tlaxcala, Mexico</strong></p>

Phaeoclavulina liliputiana is a new endemic species from Tlaxcala, from the conifer and oak forests at an altitude of 2700 m asl, characterized by a very small basidiome size and, subellipsoid and usually more or less lacrymoid spores of 4.3–6.2 × 2.7–3.5 µm, with rounded warted ornamentation. We proposed this new species based on evidence from morphological and molecular data. We provide macro- and microscopic descriptions including illustrations of the basidiocarp, scanning electron micrographs of the basidiospores and also discuss the taxonomic position of this new species. We undertook a molecular analysis using the atp6 and SSU mitochondrial loci and nuclear ribosomal LSU.

<p><strong>Three new combinations in <em>Gloeocantharellus</em> (Gomphales, Agaricomycetes) from Mexico based on molecular evidence</strong></p>

In this study, we included for the first time three Mexican Gomphaceae species in a molecular phylogeny. These species were described as members of the genus Gomphus, despite their tropical and subtropical habitat. We undertook a molecular analysis using the atp6 and SSU mitochondrial loci and nuclear ribosomal LSU. Our analysis showed that the three species studied are better included as members of Gloeocantharellus. In this study, we are suggesting three new combinations: Gloeocantharellus albidocarneus, G. calakmulensis and G. pleurobrunnescens.

Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat.

BackgroundAmong the understudied fungi found in nature are those living in close association with social and solitary bees. The bee-specialist genera Bettsia, Ascosphaera and Eremascus are remarkable not only for their specialized niche but also for their simple fruiting bodies or ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia and Ascosphaera are characterized by a unicellular cyst-like cleistothecium known as a spore cyst, while Eremascus is characterized by completely naked asci, or asci not formed within a protective ascocarp. Before molecular phylogenetics the placement of these genera within Pezizomycotina remained tentative; morphological characters were misleading because they do not produce multicellular ascocarps, a defining character of Pezizomycotina. Because of their unique fruiting bodies, the close relationship of these bee-specialist fungi and their monophyly appeared certain. However, recent molecular studies have shown that Bettsia is not closely related to Ascosphaera.In this study, I isolated the very rare fungus Eremascus fertilis (Ascomycota, Pezizomycotina) from the bee bread of honey bees. These isolates represent the second report of E. fertilis both in nature and in the honey bee hive. To establish the systematic position of E. fertilis and Bettsia alvei, I performed phylogenetic analyses of nuclear ribosomal LSU + SSU DNA sequences from these species and 63 additional ascomycetes.ResultsThe phylogenetic analyses revealed that Eremascus is not monophyletic. Eremascus albus is closely related to Ascosphaera in Eurotiomycetes while E. fertilis belongs in Myxotrichaceae, a putative member of Leotiomycetes. Bettsia is not closely related to Ascosphaera and like E. fertilis apparently belongs in Leotiomycetes. These results indicate that both the naked ascus and spore cyst evolved twice in the Pezizomycotina and in distantly related lineages. The new genus Skoua is described to accommodate E. fertilis.ConclusionsThe naked ascus and spore cyst are both shown to have evolved convergently within the bee habitat. The convergent evolution of these unusual ascocarps is hypothesized to be adaptive for bee-mediated dispersal. Elucidating the dispersal strategies of these fungal symbionts contributes to our understanding of their interaction with bees and provides insight into the factors which potentially drive the evolution of reduced ascocarps in Pezizomycotina.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0401-6) contains supplementary material, which is available to authorized users.

Molecular phylogeny and taxonomy of the genus Veloporphyrellus

Veloporphyrellus is a genus known from North and Central America, southeastern Asia, and Africa. Because species of this genus are phenotypically similar to some taxa in several genera, such as Boletellus, Leccinum, Strobilomyces, Suillus and Tylopilus s.l. belonging to Boletales, its phylogenetic disposition has never been addressed. We analyzed four DNA regions, the nuclear ribosomal LSU and tef-1α, and the mitochondrial mtSSU and atp6 genes, to investigate the phylogenetic disposition of Veloporphyrellus. Although the monophyly of the genus and its systematic placement within the Boletaceae was well supported, its relationship to other genera was not resolved. Morphologically Veloporphyrellus is distinguished from other boletoid genera by the combination of the pinkish or grayish pink hymenophore, the membranous veil hanging on the pilea margin, the trichoderm-like pileus covering and the smooth basidiospores. Five species, including two new species and two new combinations, are described and illustrated. A key to the species of Veloporphyrellus also is provided.

First Report of Persian Buttercup Downy Mildew Caused by Peronospora sp. in Korea.

Persian buttercup (Ranunculus asiaticus L.) is an ornamental plant cultivated mainly in the countries surrounding the Mediterranean Sea, and has recently become popular in Korea. During March and April 2012, Persian buttercups 'Elegance' showing symptoms of downy mildew were found in plastic greenhouses in Hwaseong City of Korea. Infection resulted in chlorotic leaves with a dark greyish and dense fungal-like growth on the lower surfaces, and finally led to necrosis of the lesions. A sample was deposited in the Korea University herbarium (KUS-F26431). Conidiophores emerging from stomata were hyaline, 250 to 550 × 7 to 15 μm, straight, and dichotomously branched in 6 to 8 orders. Ultimate branchlets were mostly in pairs, slightly curved, 5 to 15 μm long, and had obtuse tips. Conidia were brown, broadly ellipsoidal to subglobose or ellipsoidal, often pedicellated, and measured 24 to 33 × 20 to 27 μm with a length/width ratio of 1.15 to 1.30. Fourteen species of Peronospora have previously been described on the genus Ranunculus (2), of which P. ficariae was mostly considered the causal agent of downy mildew on Persian buttercup (1,3). The present Korean accession is morphologically distinct from P. ficariae on R. ficaria (a synonym of Ficaria verna) by somewhat larger conidia with often pedicel-like ends. The nuclear ribosomal LSU and ITS regions were PCR-amplified and sequenced as described in Göker et al. (4), and the resulting sequences deposited in GenBank (Accession Nos. KC111207 and JX465737, respectively). A comparison with the GenBank sequences revealed that the present Korean pathogen differed from P. ficariae on R. ficaria at 10 of 688 characters (about 1.5%) in LSU (AF119600) and 11 of 802 characters (about 1.4%) in ITS sequences (unpublished sequence). In addition, the ITS sequence exhibits a dissimilarity of 1.5 to 2.0% from three species of Peronospora parasitic on Ranunculus; P. alpicola on R. aconitifolius (AY198271), P. illyrica on R. illyricus (AY198268), and P. ranunculi on R. acris (AY198267) and R. recurvatus (AY198269). Based on morphological and molecular distinction between P. ficariae and the Korean pathogen, we provisionally indicate this pathogen as an undetermined species of Peronospora. Pathogenicity was demonstrated by shaking diseased leaves onto the leaves of healthy Persian buttercup 'Elegance', incubating the plants in a dew chamber at 20°C for 24 h, and then maintaining them in a greenhouse (20 to 24°C and relative humidity 60 to 80%). After 3 to 4 days, inoculated plants developed downy mildew symptoms, from which an identical fungus was observed, thus fulfilling Koch's postulates. Control plants treated with sterile water did not develop any symptoms of downy mildew. To our knowledge, this is the first report of a downy mildew on Persian buttercup in Asia, although this disease has been found in other continental countries, such as Italy (1), New Zealand, South Africa, and the United States (3). The presence of a downy mildew on Persian buttercup in Asia can be considered as a potentially new and serious threat to commercial production of this ornamental plant.

Lepidostroma vilgalysii, a new basidiolichen from the New World

The lichenized basidiomycete Lepidostroma vilgalysii from Mexico is described based on morphological analyses. The species is only the second representative of the family Lepidostromataceae documented from the New World, and is one of the few described lichens with an inverted morphology, with the algae in a layer at the base of the thallus. Molecular sequence data from the nuclear ribosomal LSU locus are used to confirm the placement of the holotype in Lepidostroma and to evaluate the molecular distinctiveness of the species from all other described species in the family and genus.

Morphology, vegetative and reproductive development of the red alga Portieria hornemannii (Gigartinales: Rhizophyllidaceae)

Earlier descriptions of the Indo-Pacific red alga Portieria hornemannii lacked detailed information on its vegetative and reproductive development and morphology. An in-depth treatment is presented on the development of the uniaxial thallus and the formation of male, female and tetrasporangial nemathecia. Post fertilization events and carposporophyte development is described, confirming Kylin's presumption on the development of connecting filaments between the carpogonium and the auxiliary cell following fertilization. Phylogenetic analysis using chloroplast encoded rbcL and nuclear ribosomal LSU gene sequences, including members of Rhizophyllidaceae and their close relatives suggests a monophyletic family. Contarinia is resolved as the sister taxon of a clade uniting Nesophila, Ochtodes and Portieria. The relationships among the latter genera remain largely unresolved.

Fomitiporia in sub-Saharan Africa: morphology and multigene phylogenetic analysis support three new species from the Guineo-Congolian rainforest

Fomitiporia nobilissima sp. nov., F. gabonensis sp. nov. and F. ivindoensis sp. nov., three species from the rainforest of the Guineo-Congolian phytogeographic region in Gabon, are described and illustrated. These species share a pileate basidiome, small basidiospores and an absence of setae. The critical morphological features that differentiate them are the pileus habit or shape, pore surface color, pore diameter and possibly ecology. Each new species forms distinct but closely related clades in phylogenetic analysis of DNA sequences from nuclear ribosomal LSU, ITS and translation elongation factor 1-α. Other species in sub-Saharan Africa are discussed briefly. A key to six species of Fomitiporia from sub-Saharan Africa is provided. The new combination Fomitiporia apiahyna is proposed.

Diplomitoporus rimosus is found in Asia and belongs to the Hymenochaetales

Diplomitoporus rimosus is a white rot polypore widely distributed in western N America, collected once in Africa, and is reported here from Iran. Molecular phylogenetic analyses of partial nuclear ribosomal LSU and ITS revealed that, unlike the generic type D. flavescens nested within the polyporoid clade, D. rimosus is positioned in the hymenochaetoid clade. A new genus is introduced to accommodate the species. Cyanotrama gen. nov. is recognized by its resupinate habit, narrow and strongly cyanophilous skeletal hyphae, barrel-shaped to short clavate basidia, variable presence of hyphal pegs and growth on conifers, especially Juniperus. Comparisons are made with representatives of polypores having similar morphological characteristics especially with cyanophilous skeletals. The biogeography of Cyanotrama rimosa with regard to its association with Juniperus woodlands is discussed briefly.

Two undescribed species of Phylloporia from Mexico based on morphological and phylogenetic evidence

Phylloporia rzedowskii and Phylloporia ulloai, both collected in tropical forests of the Sierra of the Huasteca Potosina, San Luis Potosi, Mexico, are described as new species. The main critical morphological features that characterize them are the pileus shape, the pore diameter, the basidiospores shape and size, and, possibly, their ecology, such as the host relationships (specificity/preference). Both species also form distinct clades in phylogenetic analysis based on partial DNA sequences data from the nuclear ribosomal LSU. An identification key for 10 species reported from the Americas is proposed.

A molecular phylogenetic study of Mannia (Marchantiophyta, Aytoniaceae) using chloroplast and nuclear markers

Phylogenetic relationships of 36 samples of Mannia and other Aytoniaceae were inferred based on sequences of the chloroplast trnL-trnF region and partial nuclear ribosomal LSU (or 26S) gene and using Targionia hypophylla and Athalamia hyalina as outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted on individual and combined molecular datasets. All phylogenetic tree topologies showed polytomies but suggest that Mannia has evolved from within Asterella and that there are two supported Mannia clades. Because Mannia is paraphyletic, with A. gracilis most closely related to M. triandra and M. pilosa, A. gracilis is transferred to Mannia. The major morphological differences between those genera are reevaluated. Based on molecular and morphological evidence Mannia is divided into the subgenera Mannia and Neesiella; Asterella subg. Graciles becomes a synonym of Mannia subg. Neesiella.

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.