| 1. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 2. |
- Abarenkov, Kessy, et al.
(författare)
-
The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 3. |
- Ariyawansa, Hiran A., et al.
(författare)
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
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Tidskriftsartikel (refereegranskat)abstract
- This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
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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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Digging Up the Roots: Taxonomic and Phylogenetic Disentanglements in Corticiaceae s.s. (Corticiales, Basidiomycota) and Evolution of Nutritional Modes
- 2021
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Corticiaceae is one of the traditional families of the Agaricomycetes and served for a long time as a convenient placement for basidiomycetes with a resupinate, corticioid form of fruiting body. Molecular studies have helped to assign many corticioid fungi to diverse families and orders; however, Corticiaceae still lacks a phylogenetic characterization and modern circumscription. Here, we provide the first comprehensive phylogenetic and taxonomic revision of the family Corticiaceae based on extensive type studies and sequences of nLSU, ITS, IGS, nSSU, and mtSSU regions. Our analyses support the recognition of ten monophyletic genera in the Corticiaceae, and show that nutritional mode is not a robust basis for generic delimitations in the family. The genus Mycobernardia and the species Corticium thailandicum, Erythricium vernum, and Marchandiomyces allantosporus are described as new to science, and five new combinations are proposed. Moreover, ancestral character state reconstruction revealed that saprotrophy is the plesiomorphic nutritional mode in the Corticiaceae, while several transitions have occurred to diverse nutritional modes in this family. Identification keys are provided to the genera in Corticiaceae s.s. as well as to the species in Corticium, Erythricium, Laetisaria, and Marchandiomyces.
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| 9. |
- 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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| 10. |
- 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
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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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