| 1. |
- Binder, M., et al.
(author)
-
The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)
- 2005
-
In: Systematics and Biodiversity. - 1477-2000. ; 3:2, s. 113-157
-
Journal article (peer-reviewed)abstract
- Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a core dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a full dataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full dataset was also analysed with the Parsimony Ratchet, using equal character weights and six-parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasidiomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea. Analyses of the full dataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasidiomycetes. Higher-level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and Jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid-phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of the major clades of Homobasidiomycetes, some of which are composed mostly or exclusively of resupinate forms (athelioid clade, corticioid clade, trechisporoid clade, Jaapia). The largest concentrations of resupinate forms occur in the polyporoid clade, russuloid clade and hymenochaetoid clade. The cantharelloid clade also includes many resupinate forms, including some that have traditionally been regarded as heterobasidiomycetes (Sebacinaceae, Tulasnellales, Ceratobasidiales). The euagarics clade, which is by far the largest clade in the Homobasidiomycetes, has the smallest fraction of resupinate species. Results of the present study are compared with recent phylogenetic analyses, and a table summarising the phylogenetic distribution of resupinate taxa is presented, as well as notes on the ecology of resupinate forms and related Homobasidiomycetes
|
|
| 2. |
- Kõljalg, Urmas, et al.
(author)
-
UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
- 2005
-
In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 166:3, s. 1063-1068
-
Journal article (peer-reviewed)abstract
- Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee.
|
|
| 3. |
- Larsson, Ellen, 1961, et al.
(author)
-
Taxomomy, ecology and phylogenetic relationships of Bovista pusilla and B. limosa in North Europe
- 2009
-
In: Mycological Progress. ; :8, s. 289-299
-
Journal article (peer-reviewed)abstract
- Bovista limosa, described from Greenland, is a species characterised by a prominent, delimited peristome and a fimbriate stoma. Morphological observations have indicated the presence of a closely related species with different peristomal characters, observations that were further confirmed through a molecular phylogenetic study of the Lycoperdaceae where deviating sequences were tentatively named Bovista cf. limosa. Here, we show that Bovista limosa as presently understood consists of two species with slightly different morphology, different habitat preferences, and different albeit overlapping distribution ranges. The two species also have clearly distinct nuclear ribosomal sequences as evidenced by an analysis of the ITS and LSU regions. We demonstrate that Bovista cf. limosa is identical to Lycoperdon pusillum described by Batsch in 1789. Batsch’s fungus has been variously interpreted and is sometimes treated as a nomen confusum. We resolve this confusion by selecting a lectotype from Batsch’s original illustrations and an epitype from the material we have sequenced. A key to the small Bovista species discussed in the paper is provided.
|
|
| 4. |
- Miller, S. L., et al.
(author)
-
Perspectives in the new Russulales
- 2006
-
In: Mycologia. - 0027-5514. ; 98:6, s. 960-970
-
Journal article (peer-reviewed)abstract
- The Russulales is one of 12 major lineages recently elucidated by molecular sequence data in the homobasidiomycetes. The order is morphologically most diverse, containing a remarkable variety of sporophore forms including resupinate, discoid, effused-reflexed, clavarioid, pileate, or gasteroid and hymenophore configurations from smooth, poroid, hydnoid, lamellate, to labyrinthoid. Functionally these fungi are primarily saprotrophs but others are ectomycorrhizal, root parasites and insect symbionts. A phylogenetic analysis of the nuclear 5.8S, ITS2 and large-subunit rDNA genes comprises the best information to date on relationships of taxa within the Russulales. Two large sister groups encompassing 11-13 major clades have been recovered within the Russulales. Based on molecular and morphological data 12 families and approximately 80 genera have been identified, although placement of many taxa has not yet been determined. The two clades containing ectomycorrhizal taxa., corresponding to the Russulaceae and the Albatrellaceae, represent the greatest diversity of sporophore morphologies. The primarily pileate lamellate family Russulaceae is nested with resupinate species and also contains pileate sequestrate, gasteroid annulate and pleurotoid forms. Albatrellaceae similarly contains resupinate poroid, pileate poroid and pileate labyrinthoid sporophores. Presence of gloeoplerous hyphae containing fluid that typically stains black in sulfoaldehyde compounds is a synapomorphy for the Russulales. Amyloid reactions in spore or hyphal walls that occur frequently throughout the Russulales often are perceived as an obvious synapomorphy but are inconsistent. Approaches including sequencing functional genes, analysis of gene expression and biochemical analysis across the entire order are needed.
|
|
| 5. |
- Moncalvo, J. M., et al.
(author)
-
The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods
- 2006
-
In: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 98:6, s. 937-948
-
Journal article (peer-reviewed)abstract
- We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.
|
|
| 6. |
- Niemelä, T., et al.
(author)
-
Anomoloma, a new genus separated from Anomoporia on the basis of decay type and nuclear rDNA sequence data
- 2007
-
In: Mycotaxon. - 0093-4666. ; 100, s. 305-317
-
Journal article (peer-reviewed)abstract
- Five species of Anomoporia, and related but deviating material from South China, were studied microscopically and sequenced. Bayesian and maximum parsimony analyses were conducted using nuclear ribosomal ITS and large-subunit DNA regions. The species belong to a subclade within or close to the euagarics clade. The brown-rot-causing species A. bombycina (type of the genus Anomoporia), A. vesiculosa, and A. kamtschatica belong to a genus complex together with Ceraceomyces, Hypochniciellum, Irpicodon and Plicaturopsis, but their inner hierarchy needs further study before conclusions on genus limits can be made. Four strongly rhizomorphic species of Anomoporia are associated with white-rot, and they were found to form a well-supported clade. Consequently, a new genus Anomoloma is described. The following new combinations are made: Anomoloma albolutescens (type of the genus), A. myceliosum, A. flavissimum, and a new species is described from the South Chinese material: A. rhizosum. Numerous new records of A. flavissimum expand considerably its known range in China.
|
|
| 7. |
|
|
| 8. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)
- 2006
-
In: Mycological Research. - : Elsevier BV. - 0953-7562. ; 110, s. 1426-1432
-
Journal article (peer-reviewed)abstract
- Fruiting body guided sequence analysis of mycorrhizal root-tip mycelia is a powerful yet relatively sparsely explored method for species-level identification of mycorrhizal fungi. It is used in this study to indicate mycorrhizal associations in the corticioid (resupinate) genus Sistotrema of the cantharelloid clade through phylogenetic analysis of the ITS and nuLSU rDNA regions of two spatiotemporally co-occurring Sistotrema fruiting bodies and ectomycorrhizal root tips. The genus Sistotrema is confirmed to be polyphyletic, and the mycorrhizal species form a strongly supported monophyletic clade together with the stipitate genus Hydnum. The remaining lineages of Sistotrema may well be saprotrophic, the nutritional mode traditionally attributed to the genus, but the phylogenetic analyses show that they should be excluded from Sistotrema. The cantharelloid clade contains several mycorrhizal genera, but no symbiotic associations have previously been demonstrated for Sistotrema. (c) 2006 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
|
|
| 9. |
- Sjökvist, Elisabet, 1982, et al.
(author)
-
A multi-locus phylogeny of the Polyporales
- 2009
-
In: Abstract Book, Botany & Mycology, Snowbird, Utah, July 25-29. ; 2009
-
Conference paper (other academic/artistic)abstract
- The recently redefined order Polyporales consists of roughly 1800 species of primarily polyporoid and corticioid fungi. Previous studies on the polyporoid clade have only used sequences from one or a few rDNA genes, resulting in phylogenies with low support on branches. This study aims to identify higher-level relationships within Polyporales using multi-locus phylogenies. For this purpose two matrices were composed. One is a matrix with gene markers RPB2, EF1-α, nLSU, 5.8S and mtSSU, for 53 in-group taxa. The other a super-matrix with RPB2, EF1-α, SSU, nLSU, 5.8S, mtSSU, and ATP6, for 84 in-group taxa. Preliminary analyses on the smaller dataset result in a strong support for the order in Bayesian analysis, but with only moderate support in Jackknife analysis. Several high-support clades could be identified in both analyses, which we temporarily acknowledge as Byssomeruliaceae, Fomitopsidaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae and Steccherinaceae. However, several taxa remain that in Bayesian analysis show little affinity to other taxa, and in Jackknife analysis little or no affinity to other taxa. The commonly identified Antrodia clade, core polyporoid clade, phlebioid clade and residual polyporoid clade are discussed. This study is the first to present a comprehensive family-level multi-locus phylogeny of the Polyporales.
|
|
| 10. |
- Vasiliauskas, R., et al.
(author)
-
Persistence and long-term impact of Rotstop biological control agent on mycodiversity in Picea abies stumps
- 2005
-
In: Biological Control. - : Elsevier BV. - 1049-9644. ; 32:2, s. 295-304
-
Journal article (peer-reviewed)abstract
- To prevent infection by the root rot fungi Heterobasidion spp., surfaces of freshly cut Picea abies stumps are sprayed with Rotstop biocontrol agent, which constitutes a spore suspension of a single genotype of the competitive fungus Phlebiopsis gigantea. In Fennoscandia, the agent is applied on 47,000 ha of forestland yearly. The aims of the present work were to estimate the persistence of Rotstop P. gigantea strain and its impact on mycodiversity in 4- to 6-year-old P. abies stumps. Fungal isolation was done from 947 wood samples taken from 130 stumps, 60 of which were Rotstop-treated and 70 were untreated controls. Half of the stumps were 4-year, and another half 6-year-old. 705 fungal strains representing 81 species were isolated. Species richness was lower in Rotstop-treated stumps, both after 4 (by 32%; P = 0.08) and after 6 years (46%; P = 0.01). The majority of species (6575%) isolated from Rotstop-treated stumps were also found in controls. In 4-year-old Rotstop-treated stumps, the fungal community was dominated by P. gigantea, both in terms of isolated strains and observed fruitbodies. Of P. gigantea isolates, only Rotstop genotypes were found in treated stumps, while control stumps harboured wild strains of the species. In 6-year-old both treated and control stumps, P. gigantea was seldom detected and no fruitbodies were observed. Here, the occurrence of other fungi increased, e.g., Resinicium bicolor, Sistotrema brinkmannii, and Hypholoma capnoides. The pathogen, Heterobasidion spp., was the only basidiomycete with a significantly reduced incidence in Rotstop-treated stumps
|
|
