| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation
- 2011
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Ingår i: Mycoscience. - : The Mycological Society of Japan. - 1340-3540 .- 1618-2545. ; 52:4, s. 278-282
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Tidskriftsartikel (refereegranskat)abstract
- Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.
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| 2. |
- Urbina, Hector, et al.
(författare)
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DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico
- 2016
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Ingår i: Mycoscience. - : The Mycological Society of Japan. - 1340-3540 .- 1618-2545. ; 57:3, s. 217-227
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Tidskriftsartikel (refereegranskat)abstract
- Soil fungal communities in tropical regions remain poorly understood. In order to increase the knowledge of diversity of soil-inhabiting fungi, we extracted total DNA from top-organic soil collected in seven localities dominated by four major ecosystems in the tropical island of Puerto Rico. In order to comprehensively characterize the fungal community, we PCR-amplified the internal transcribed spacer 2 (ITS2) fungal barcode using newly designed degenerated primers and varying annealing temperatures to minimize primer bias. Sequencing results, obtained using Ion Torrent technology, comprised a total of 566,613 sequences after quality filtering. These sequences were clustered into 4140 molecular operational taxonomic units (MOTUs) after removing low frequency sequences and rarefaction to account for differences in read depth between samples. Our results demonstrate that soil fungal communities in Puerto Rico are structured by ecosystem. Ascomycota, followed by Basidiomycota, dominates the diversity of fungi in soil. Amongst Ascomycota, the recently described soil-inhabiting class Archaeorhizomycetes was present in all localities, and taxa in Archaeorhizomycetes were among the most commonly observed MOTUs. The Basidiomycota community was dominated by soil decomposers and ectomycorrhizal fungi with a distribution strongly affected by local variation to a greater degree than Ascomycota.
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| 3. |
- Larsson, Ellen, 1961, et al.
(författare)
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Inocybe praetervisa group - A clade of four closely related species with partly different geographical distribution ranges in Europe
- 2018
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Ingår i: Mycoscience. - : The Mycological Society of Japan. - 1340-3540. ; 59:4, s. 277-287
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Tidskriftsartikel (refereegranskat)abstract
- Sequence data from a broad geographical region and different habitats show that the Inocybe praetervisa clade is comprised of four closely related species. These species of section Marginatae are characterized by having nodulose spores and a stipe that is abundantly pruinose only in the upper half. Inocybe praetervisa occurs in Southern Europe in mountainous mixed coniferous forests, and is not confirmed from Northern Europe. Inocybe rivularis occurs in northern boreal forests up to the lower alpine zone, associated with Betula in moist habitats, and is not confirmed from Southern Europe. Inocybe taxocystis is confirmed as a later synonym of I. favrei. The species has a wide geographical distribution range in Europe, mainly restricted to the alpine zone and moist soils, associated with Salix herbacea. Inocybe arctica is here described as a new species. It occurs in the arctic and higher alpine zones, associated with Dryas octopetala, Salix polaris, S. reticulata and S. herbacea. All species except I. arctica are shown to have an intercontinental distribution range and are confirmed from North America. Sequence data suggest the occurrence of one additional species in the alpine zone of China. A key to the species in the I. praetervisa group is provided. (C) 2017 The Mycological Society of Japan. Published by Elsevier B.V. All rights reserved.
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