| 1. |
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| 2. |
- Bok, Gunilla, 1961, et al.
(författare)
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Mass occurrence of Penicillium corylophilum in crawl spaces, south Sweden
- 2009
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Ingår i: Building and Environment. - 0360-1323. ; 44, s. 2413-2417
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Tidskriftsartikel (refereegranskat)abstract
- Buildings with crawl space foundations are looked upon as high-risk constructions with respect to mould growth, especially on the blind floor. This mould growth can be extensive and cover several square meters of the blind floor with potential health risks as a consequence. Mould occurrence and mould species diversity were investigated in a large small-house area in the south of Sweden, comprising 212 buildings. The crawl spaces were inspected and samples from the blind floor were taken. The relative humidity was measured and reached 80–100% for several consecutive months. Subsets of the samples were cultured and the fungi isolated were further analyzed by sequencing of the Internal Transcribed Spacer (ITS) region of nuclear ribosomal Deoxyribo Nucleic Acid (DNA). The results were compared with results from other, relevant studies and confirm that Penicillium corylophilum is the completely dominating mould species in crawl spaces. The occurrences could not be explained as accidental since the extensive occurrence in many dwellings had developed over several years.
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| 3. |
- Dai, Y. C., et al.
(författare)
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Ganoderma lingzhi (Polyporales, Basidiomycota): the scientific binomial for the widely cultivated medicinal fungus Lingzhi
- 2017
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 16:11-12, s. 1051-1055
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Tidskriftsartikel (refereegranskat)abstract
- The traditional medicinal fungus, Lingzhi, has long been considered to be Ganoderma lucidum, but was recently described as G. lingzhi based on both morphological and molecular data. Months earlier than this description, the species was identified as G. sichuanense by another research group. A sequenced epitype for G. sichuanense was selected that, if accepted, meant that it became a synonym of, and an earlier name for, G. lingzhi. However, the holotype of G. sichuanense is well developed with distinct morphological characters, and its ITS sequence, the DNA barcode for fungal taxonomy, is available. The holotype of G. sichuanense does not possess the typical morphological characteristics of Lingzhi, and the designated epitype is not conspecific with the holotype from morphological, phylogenetic and ecological perspectives. Consequently, the designation of the epitype is considered to conflict with the regulations of the Code and should be rejected. As no other previously published species name matches Lingzhi, the correct name for this fungus is G. lingzhi.
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| 4. |
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| 5. |
- Ghobad-Nejhad, Masoomeh, et al.
(författare)
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A first annotated checklist of corticioid and polypore basidiomycetes of the Caucasus region
- 2010
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Ingår i: Mycologia Balcanica. - 1312-3300. ; 6, s. 123-168
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Tidskriftsartikel (refereegranskat)abstract
- Abstract. This is the first checklist from the territories in the Caucasus region, including Armenia, Azerbaijan, Georgia, Russian Caucasus, NE Turkey, and N–NW Iran. Altogether 349 corticioid and 246 polypore species are known from the area, 74 of which are reported as new to the entire region. Each record includes literature references, and, when available, selected unpublished specimens deposited in herbaria or collected recently are listed. The distribution of each species in the Caucasian countries is summarized, and brief notes are provided for some species. Finally, a table and a diagram representing the number of corticioids and polypores and the ratio of these in each country are provided. The checklist aims to serve as a baseline for more detailed studies on wood-inhabiting basidiomycetes in the Caucasus region. The importance of this catalogue for fungal conservation is also mentioned.
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| 6. |
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| 7. |
- Ghobad-Nejhad, Masoomeh, 1978, et al.
(författare)
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Checklist of Iranian non-gilled/non-gasteroid hymenomycetes (Agaricomycotina)
- 2012
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Ingår i: Mycotaxon. - : Mycotaxon, Ltd.. - 0093-4666 .- 2154-8889. ; 119
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT — This list includes 395 species of Iranian non-gilled/non-gasteroid hymenomycetes. Corticioid, poroid (polypores), hydnoid, clavarioid, cantharelloid, thelephoroid, and cyphelloid fungi are covered, together with heterobasidiomycetes. Almost all the species are supported by at least one herbarium specimen. The list has been compiled mainly from material collected by the authors, verified reports and literature. Nineteen species are reported for the first time from the country, and 118 species are added to the most recent account of aphyllophoroid fungi of North Iran by Hallenberg (1981, Mycotaxon 12: 473–502). The occurrence in Iran of six species is regarded as doubtful, while 12 species are excluded. The number of species known for each province in Iran is listed, with Golestan shown to be the most species-rich province. The total number of species recognized for major Iranian phytogeographical territories is also noted and Funalia trogii, Inonotus hispidus, and Schizophyllum commune are shown to be the most widespread species. A permanent repository for continuous updates has been made available via the Myco-Lich website, and future new records for the country will be published online. Users can access the latest changes to the checklist via subscription to a feed (RSS). The link to the checklist is http://www.myco-lich.com/mycologyof- iran/basidiomycota/checklists/National-checklist.
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| 8. |
- Ghobad-Nejhad, Masoomeh, et al.
(författare)
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Erythricium atropatanum sp. nov. (Corticiales, Basidiomycota) from Iran, based on morphological and molecular data
- 2011
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Ingår i: Mycological Progress. - 1617-416X. ; 10, s. 61-66
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 9. |
- Ghobad-Nejhad, Masoomeh, et al.
(författare)
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Multiple evidence for recognition of Phlebia tuberculata, a more widespread segregate of Phlebia livida (Polyporales, Basidiomycota)
- 2012
-
Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 11:1, s. 27-35
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Tidskriftsartikel (refereegranskat)abstract
- It has been previously shown that the Phlebia livida complex consists of two incompatible subspecies, viz. ssp. livida and ssp. tuberculata. Here we explain that the two subspecies can be distinguished based on morphology, phylogenetic analyses of nuclear ITS sequences, genetic distance, and a haplotype network, as well as by substrate preference. Subspecies tuberculata is raised to specific rank and a thorough description is provided. According to the results of the network analysis, Phlebia tuberculata comb. nov. seems to be an older species than Phlebia livida, congruent with its wider distribution, and at least some of its present populations have spread from the Caucasus region since the last glaciation. A key to the species of the Phlebia livida complex is presented
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| 10. |
- Ghobad-Nejhad, Masoomeh, et al.
(författare)
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Phylogeny and taxonomy of the genus Vuilleminia (Basidiomycota) based on molecular and morphological evidence, with new insights into Corticiales
- 2010
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Ingår i: TAXON. - 0040-0262. ; 59:5, s. 1519-1534
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Tidskriftsartikel (refereegranskat)abstract
- Vuilleminia is a corticioid genus common in Europe whose species inhabit decaying and dead attached wood of angiosperms. To examine the circumscription of the genus and the phylogenetic relationships among its species, we analyzed nuclear ribosomal sequence data from the ITS region and the LSU gene with maximum parsimony and Bayesian methods and also studied morphological characters. Our results challenge the notion that spore size and host specificity are critically important factors in delimiting species of Vuilleminia. A taxonomic summary of the accepted species in Vuilleminia is provided. Vuilleminia species described from the South America and Africa are demonstrated to be distinct from those of the north temperate region. Australovuilleminia coccinea gen. & sp. nov. is proposed for the taxon previously reported as V. comedens from New Zealand. Punctulariopsis gen. nov. is proposed for V. subglobispora described from Argentina (= Punctulariopsis subglobispora) and V. obducens from Ethiopia (= Punctulariopsis obducens). Vuilleminia is shown to be a monophyletic genus, apparently north hemispheric, and currently comprises six species. Vuilleminia together with the closely related genera Cytidia and Australovuilleminia form a well-supported clade (Vuilleminia clade) and the family name Vuilleminiaceae is resurrected to recognize this clade. Vuilleminia quercina (= Corticium quercicola) is not closely related to the other Vuilleminia species and is instead nested in a completely different clade (Corticium clade). A new genus Marchandiopsis is erected for this taxon.
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| 11. |
- Ghobad-Nejhad, Masoomeh, et al.
(författare)
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The Caucasian corticioid fungi: level of endemism, similarity and possible contribution to European fungal diversity
- 2012
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 52:1, s. 35-48
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Tidskriftsartikel (refereegranskat)abstract
- We assess the composition of corticioid fungi inthe Caucasus region for the first time. The Caucasiancorticioids were compared with those of well-documentedareas in the Northern Hemisphere using the Tripartitesimilarity index and cluster analysis. To investigate thesignificance of the Caucasus region as a possible contributorto the colonization of wood-inhabiting basidiomycetesin Europe, DNA sequences of nuclear ribosomal internaltranscribed spacers (ITS1 and ITS2) belonging to thecorticioid fungus Peniophorella praetermissa were analysedfor comparisons of genetic diversity within anddifferentiation between geographical regions. Putativespecies endemism and disjunction of corticioids in theCaucasus region is also discussed. The composition ofcorticioid fungi in the Caucasus region was found to bedistinctly more similar to Europe and North America thanto East Asia and India. Similarity tests and molecular Fstsboth point to a strong connection between the Caucasus andEurope. The highest molecular diversity in P. praetermissawas in the Caucasus and East Asia as compared with otherregions studied. The Caucasus and East Asia weresignificantly differentiated from each other, and unlikeCaucasian samples, East Asian sequences were highlydivergent from the European ones. This result suggests thatthe Caucasus might have been a source of colonization forEurope. Endemism is very low, possibly a common featurefor wood-inhabiting saprotrophic fungi.
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| 12. |
- Gorjón, Sergio Pérez, et al.
(författare)
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A survey of the corticioid fungi from the Biosphere reserve of Las Batuecas-Sierra de Francia (Spain)
- 2009
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Ingår i: Mycotaxon. ; , s. 161-164
-
Tidskriftsartikel (refereegranskat)abstract
- The Natural Park of “Las Batuecas-Sierra de Francia”, recently declared Biosphere Reserve in 2006, is situated in the south of Salamanca province in the central and occidental part of the Iberian Peninsula (40º 26' and 40º 35 N latitude, 5º 57' and 6º 15' W longitude) with and extension of 320 km2. The area presents a typical Mediterranean humid climate and the next main forest formations are present: deciduous forests of Quercus ilex subsp. ballota (Desf.) Samp., Quercus suber L., Quercus faginea Lam., Quercus pyrenaica Willd., Quercus robur L., Castanea sativa Mill., Arbutus unedo L., Eucalyptus camaldulensis Denhn.; coniferous forests of Pinus pinaster Aiton, Pinus sylvestris L., Juniperus oxycedrus L.; riparian formations of Alnus glutinosa (L.) Gaertn., Salix spp. and Populus spp., among others. Despite of its Biosphere Reserve declaration (mainly based on the interesting mediterranean vegetal and animal communities and socio-cultural patrimony) there are really few fungal studies in the area and this is the first long term systematized study regarding corticioid fungi.
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| 13. |
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| 14. |
- Gorjon, Sergio Perez, et al.
(författare)
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Some new species and a first checklist of corticioid fungi (Basidiomycota) from Chile
- 2013
-
Ingår i: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 12:2, s. 185-192
-
Tidskriftsartikel (refereegranskat)abstract
- Gloeocystidiellum rajchenbergii, Hypochnicium patagonicum, Pteridomyces valdivianus, and Stereum greslebinii are described as new species from the Chilean Patagonia. An annotated checklist of corticioid fungi from Chile, listing 94 species with notes on distribution and ecology, scheduled for regular update, is available from http://corticioids.webs.com/checklists.htm.
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| 15. |
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| 16. |
- Hallenberg, Nils, 1947
(författare)
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FCUG culture collection, summary of results during 30 years (1098 - 2010)
- 2011
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Ingår i: Synopsis Fungorum. ; 29, s. 82-200
-
Forskningsöversikt (refereegranskat)abstract
- Fungal Cultures of University of Gothenburg has closed down. A great part of the cultures have now been transferred to CBS, Utrecht, and given new CBS-numbers. The Caucasus area has been intensively sampled and duplicates of those cultures have been transferred to the fungus collection at Iranian Research Institute of Plant Protection (IRAN), Tehran. In all, the FCUG collection contained about 10.000 strains, representing ca 3000 specimens and 500 species. Almost all species were wood-inhabiting basidiomycetes, mainly belonging to the artificial group “Corticiaceae”. A summary is given below for all specimens where some useful kind of data exists today. This includes 1) all specimens transferred to CBS and IRAN, 2) all specimens for which crossing test data exist, 3) and all specimens for which DNA sequences have been obtained. Moreover, herbarium data are provided so all FCUG numbers should be possible to link to a voucher, in most cases deposited at GB.
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| 17. |
- Hallenberg, Nils, 1947
(författare)
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Leptocorticium tenellum (Agaricomycetes) found in Chile
- 2012
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Ingår i: Kurziana. - 0075-7314. ; 37:1, s. 109-112
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Tidskriftsartikel (refereegranskat)abstract
- The corticioid fungus Leptocorticium tenellum was recently found in Puyehue National Park, Chile. Earlier records of the species are from Colombia and Venezuela. The species is described and illustrated, and the biogeography of the genus is discussed.
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| 18. |
- Hallenberg, Nils, 1947
(författare)
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Our Peniophora aspects
- 2013
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Ingår i: Omphalina. - 1925-1858. ; IV:5, s. 6-9
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 19. |
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| 20. |
- Hallenberg, Nils, 1947
(författare)
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Peniophora cinerea and its allies
- 2013
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Ingår i: Omphalina. - 1925-1858. ; IV:5, s. 10-11
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 21. |
- Hallenberg, Nils, 1947, et al.
(författare)
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Peniophora pseudonuda is a synonym to P. laeta
- 2010
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Ingår i: Mycotaxon. - 0093-4666. ; 112, s. 153-162
-
Tidskriftsartikel (refereegranskat)abstract
- Abstract — Peniophora laeta is easily recognized because it is restricted to Carpinus as host in Europe, and the reddish yellow fruitbody is provided with prominent teeth or hyphal pegs, disrupting the bark when developing. P. pseudonuda was earlier not even thought of as related to P. laeta, because fruitbodies are smooth and developing on the bark. Moreover, fruitbody initiation starts with a thin layer of brown-pigmented hyphae on bark surface. This render a bluish tint to the mature fruitbody which is in striking contrast to the orange-yellow basidiomata found in P. laeta. Nevertheless, both ITS sequences and crossing tests show that P. pseudonuda is conspecific with P. laeta. This was confirmed also by similarity in spore, basidia and cystidia morphology.
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| 22. |
- Hallenberg, Nils, 1947, et al.
(författare)
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Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
- 2008
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Ingår i: Botany. - 1916-2804. ; 86:11, s. 1319-1325
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Tidskriftsartikel (refereegranskat)abstract
- The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.). Key words: Polyporales, Radulodon, phylogeny, plant interactions. Résumé: Le Pseudolagarobasidium (Polyporales, Basidiomycota) constitue un genre de petits champignons résupinés qui comporte actuellement cinq espèces, toutes décrites à partir de régions tropicales ou subtropicales, incluant deux espèces parasites des racines d'arbres de la famille des légumineuses. On en a récemment établi la synonymie avec le genre Radulodon sur la base morphologique, mais les auteurs utilisent ici l'approche moléculaire. On constate que le genre Pseudolagarobasidium constitue un groupe monophylétique robuste excluant les Radulodon ce qui conduit au rejet de cette synonymie. L'amplitude écologique du genre va du saprophytisme au parasitisme, et on présente des preuves qu'au moins une lignée est un endophyte du cacaoyer (Theobroma cacao L.). Mots-clés : Polyporales, Radulon, phylogénie, interactions végétales.
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| 23. |
- Hallenberg, Nils, 1947, et al.
(författare)
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Species complexes in Hericium (Russulales, Agaricomycota) and a new species - Hericium rajchenbergii - from southern South America
- 2013
-
Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 12:2, s. 413-420
-
Tidskriftsartikel (refereegranskat)abstract
- Species of the genus Hericium are generally recognized by macro morphology of their basidiomes, while they are very similar in the microscope. As a result, species boundaries are not always clear, and many collections are subsumed under incorrect names. We report on a thorough phylogenetic analysis based on ITS sequences to clarify the application of the most common names in the genus. H. alpestre, H. americanum, and H. erinaceus cannot readily be distinguished by their ITS sequences alone, while they are kept separate by characters from substrate preferences, geographical distribution, and macro morphology. A neotype is selected for H. alpestre. A well supported clade includes H. coralloides together with other, unnamed taxa. One of these, H. rajchenbergii from Argentina, is here described as new to science.
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| 24. |
- Hallenberg, Nils, 1947, et al.
(författare)
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The Peniophorella praetermissa species complex (Basidiomycota)
- 2007
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Ingår i: Mycological Research. - : Elsevier BV. - 0953-7562. ; 111:12, s. 1366-1376
-
Tidskriftsartikel (refereegranskat)abstract
- The corticioid basidiomycete Peniophorella praetermissa has long been regarded as a morphologically variable species complex. An ITS-based phylogenetic study based on a worldwide sampling was carried out using parsimony and Bayesian inference. The resulting trees feature three major clades, further divided into well-supported subclades. These could be considered as distinct species, a contention that is further supported by crossing test data. Only two out of the eight phylogenetic lineages identified can be distinctly morphologically characterized: P. odontiaeformis and P. subpraetermissa. P. odontiaeformis is an odontioid species with a paleotropical distribution whereas the taxa in the remaining subclades have smooth basidiomata and are distributed in temperate areas. P. subpraetermissa is known only from the type collection and is distinguished microscopically by its reddish brown apically encrustated cystidia. Taxa in the remaining subclades are impossible to distinguish from each other morphologically, and therefore, are viewed as a species complex, P. praetermissa s. lat. One of the subclades, which is widely distributed but restricted to the Northern hemisphere, is proposed to represent P. praetermissa s. str. An epitype is selected from the same area as the holotype, among the specimens studied here. However, the geographically most widespread clade with many representatives from both hemispheres is here referred to as P. pertenuis, a taxon that was previously considered a synonym to P. praetermissa.
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| 25. |
- Hembrom, M. E., et al.
(författare)
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Morphology and phylogeny reveal a novel hydnoid taxon from India: Mycorrhaphoides stalpersii gen. and sp. nov
- 2017
-
Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X. ; 35:1, s. 85-94
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Tidskriftsartikel (refereegranskat)abstract
- Mycorrhaphoides gen. nov. and Mycorrhaphoides stalpersii sp. nov. are described and defined based on morphological details and phylogenetic inference of a hydnoid macrofungus collected in Acharya Jagadish Chandra Bose Indian Botanic Garden, Howrah (India). It is characterized by stipitate basidiomata with duplex context in stipe, presence of multi-clamped septa, and smooth and hyaline cystidia.
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| 26. |
- Jang, Yeongseon, et al.
(författare)
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Hypochnicium pini, a new corticioid basidiomycete in East Asia
- 2013
-
Ingår i: Mycotaxon. - 0093-4666. ; 124, s. 209-217
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Tidskriftsartikel (refereegranskat)abstract
- A new species, Hypochnicium pini, is described based on morphological and molecular characters. This species was collected in Seoul, Korea, and Hubei, China. It belongs to the H. punctulatum group and has a morphology quite similar to its sister taxon, H. cremicolor. However, the basidiome thickness, cystidial size, and ITS region sequences differentiate H. pini from H. cremicolor. Detailed description and illustration of H. pini are presented and a key to Korean species of Hypochnicium is provided.
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| 27. |
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| 28. |
- Kaur, J., et al.
(författare)
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Cristinia tubulicystidiata sp nov from India
- 2014
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Ingår i: Mycotaxon. - : Mycotaxon, Ltd.. - 0093-4666 .- 2154-8889. ; 127, s. 89-92
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Tidskriftsartikel (refereegranskat)abstract
- A new corticioid species, Cristinia tubulicystidiata, is described from the Kalatop area, Chamba (Himachal Pradesh), India.
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| 29. |
- Kauserud, H., et al.
(författare)
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Hybridization among cryptic species of the cellar fungus Coniophora puteana (Basidiomycota)
- 2007
-
Ingår i: Molecular Ecology. - 0962-1083. ; 16:2, s. 389-399
-
Tidskriftsartikel (refereegranskat)abstract
- In this study we have analysed the genetic variation and phylogeography in a global sample of the cellar fungus Coniophora puteana, which is an important destroyer of wooden materials indoor. Multilocus genealogies of three DNA regions (beta tubulin, nrDNA ITS and translation elongation factor 1α) revealed the occurrence of three cryptic species (PS13) in the morphotaxon C. puteana. One of the lineages (PS3) is apparently restricted to North America while the other two (PS12) have wider distributions on multiple continents. Interspecific hybridization has happened between two of the lineages (PS1 and PS3) in North America. In three dikaryotic isolates, two highly divergent beta tubulin alleles coexisted, one derived from PS1 and one from PS3. Furthermore, one isolate included a recombinant ITS sequence, where ITS1 resembled the ITS1 version of PS3 while ITS2 was identical to a frequent PS1 ITS2 version. This pattern must be due to hybridization succeeded by intralocus recombination in ITS. The results further indicated that introgression has happened between subgroups appearing in PS1. We hypothesize that the observed reticulate evolution is due to previous allopatric separation followed by more recent reoccurrence in sympatry, where barriers to gene flow have not yet evolved. A complex phylogeographical structure is observed in the morphotaxon C. puteana caused by (i) cryptic speciation; (ii) the interplay between natural migration and distribution patterns and probably more recent human mediated dispersal events; and (iii) hybridization and introgression
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| 30. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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A software pipeline for processing and identification of fungal ITS sequences
- 2009
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Ingår i: Source Code for Biology and Medicine. - 1751-0473. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. Results The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50 % of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10 % of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. Conclusions The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
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| 31. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 32. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
- 2008
-
Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 2008:4, s. 193-201
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Tidskriftsartikel (refereegranskat)abstract
- The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequencebased mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3 % threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITSbased species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
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| 33. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data
- 2003
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Ingår i: Mycologia. ; 95:1, s. 54-50
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Tidskriftsartikel (refereegranskat)abstract
- Parsimony analysis based on ITS sequence data was carried out to investigate the Hypochnicium punctulatum complex (Basidiomycota). The study gives full support to earlier, crossing test-based species delimitations. Altogether, 18 specimens were sequenced and their spore sizes plotted together with measurements from the corresponding type specimens. Spore sizes were found to cluster readily into four groups, all of which were supported by the phylogenetic analysis. However, in the case of H. punctulatum and H. albostramineum, the morphological delimitation is unsatisfactory and a zone of potential spore size overlap is shown to exist. The new combination Hypochnicium cremicolor is proposed for a species previously known as a small-spored taxon in the H. punctulatum complex, and H. caucasicum is shown to be a younger synonym to H. wakefieldiae. A key to the species is provided.
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| 34. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere
- 2003
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Ingår i: Mycological Research. ; 107:6, s. 645-652
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies of morphological variation in the homobasidiomycete Hyphoderma setigerum have lead to suspicions of a species complex. This study explores variation in DNA sequences from the nuclear ribosomal ITS region of 45 specimens from America, Asia, and Europe in a phylogeographic context. Based on molecular analysis, morphological studies, and crossing tests, nine preliminary taxa are shown to exist inside the species complex, and the two previously described segregate species H. subsetigerum and H. nudicephalum are confirmed. The molecular analysis shows evidence of allopatric differentiation over intercontinental distances. Only one of the nine well-supported clades has a geographic distribution spanning more than one continent, probably indicating the importance of vicariance in the evolution of this species complex. The basionym of H. setigerum, Thelephora setigera, is neotypified to fix the application of that name.
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| 35. |
- Paulus, B., et al.
(författare)
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Phylogenetic studies in Hypochnicium (Basidiomycota), with special emphasis on species from New Zealand
- 2007
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Ingår i: New Zealand Journal of Botany. - 0028-825X. ; 45:1, s. 139-150
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomic and phylogenetic affiliation of Hypochnicium specimens from New Zealand were studied using morphological and molecular analyses. Phylogenetic analyses based on ITS region of rDNA suggest that species within Hypochnicium form a monophyletic group with respect to outgroups. The synonymy of Gyrophanopsis with Hypochnicium is validated and the genus Nodotia is re-evaluated as a synonym of Hypochnicium. Sequence analyses of H. zealandicum and a specimen within the H. punctulatum complex from New Zealand place both as sister taxa of H. polonense and H. cremicolor, respectively. Although spore dimensions of H. zealandicum overlap with those of H. polonense, it is currently retained as a separate species on the basis of geographical separation and phylogenetic analysis. New Zealand specimens recorded as H. punctulatum represent a new species, which is described and illustrated as H. aotearoae.
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| 36. |
- Telleria, M. Teresa, et al.
(författare)
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A reevaluation of Hypochnium (Polyporales) based on morphological and molecular characters
- 2010
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Ingår i: Mycologia. - 0027-5514. ; 102:6, s. 1426-1436
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: Hypochnicium is a genus of corticioid, wood-inhabiting fungi in the Polyporales with a worldwide distribution. The genus has been characterized by the nature of the spores: thick-walled, smooth or ornamented, and cyanophilous. Nine new ITS nrDNA sequences from species of this genus were aligned with 32 sequences obtained from GenBank and phylogenetic analyses were performed. The species of Hypochinicum were resolved as monophyletic using two Hyphoderma species as out-group. Four well-supported clades were determined within the genus: one contains taxa with smooth spores and the other three species with ornamented spores. Hypochnicium albostramineum is closely related to H. wakefieldiae, but new evidence shows that the two species are morphologically difficult to distinguish from each other. Hypochnicium versatum must be included in Gloeohypochnicium and the new combination Gloeohypochnicium versatum is proposed. Two new species, Hypochnicium michelii from Spain, and Hypochnicium guineensis, from Equatorial Guinea, are described.
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| 37. |
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| 38. |
- Wu, Sheng-Hua, et al.
(författare)
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The white-rotting genus Phanerochaete is polyphyletic and distributed throughout the phleboid clade of the Polyporales (Basidiomycota)
- 2010
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 42, s. 107-118
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Tidskriftsartikel (refereegranskat)abstract
- Abstract The genus Phanerochaete (Polyporales, Basidiomycota) has traditionally been delimited based on the gross morphology of the fruiting body and on the nature of the hyphal structure, cystidia, and spores. However, several recent studies based on molecular data indicate that the genus is polyphyletic as presently circumscribed, although most of its species are found in the phlebioid clade of the Polyporales. To further our understanding of the genus, 54 new sequences from the large subunit of the nuclear ribosomal DNA of 45 previously unsequenced Phanerochaete species were obtained and analyzed jointly with a large selection of taxa in the phlebioid clade. The results show that there is a well-supported Phanerochaete core group that includes the type species Phanerochaete velutina (the currently accepted name of the generic type, Thelephora alnea). Representatives of a few satellite genera, including Hjortstamia, Phlebiopsis, and Rhizochaete, are found in the immediate topological vicinity of Phanerochaete. Outside the core group but still within the phlebioid clade are several taxa that have been referred to as members of Phanerochaete by some authors but that are here assigned to at least five different monophyletic clades. Phanerochaete viticola is found in the Hymenochaetales and is shown to have phylogenetic affinities to the partially symbiotic Rickenellaceae. A new genus, Ginnsia, is erected for this species, and the new combinations Ginnsia viticola, Hjortstamia brunneocystidiata, H. laxa, and Phlebiopsis lamprocystidiata are proposed. A denser taxon and gene sampling in the phleboid clade will be needed to settle the precise taxonomic affiliation of many of the species presently referred to as Phanerochaete, and numerous nomenclatural changes are doubtlessly looming on the horizon.
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| 39. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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