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      New light on names and naming of dark taxa

      research-article
      1 , 2 , 3
      MycoKeys
      Pensoft Publishers
      Taxonomy, nomenclature, mycology, biodiversity

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          Abstract

          Abstract

          A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as “dark taxa” or “dark matter fungi”. As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

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          Most cited references24

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          Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

          Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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            Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi.

            Estimates suggest that only one-tenth of the true fungal diversity has been described. Among numerous fungal lineages known only from environmental DNA sequences, Soil Clone Group 1 is the most ubiquitous. These globally distributed fungi may dominate below-ground fungal communities, but their placement in the fungal tree of life has been uncertain. Here, we report cultures of this group and describe the class, Archaeorhizomycetes, phylogenetically placed within subphylum Taphrinomycotina in the Ascomycota. Archaeorhizomycetes comprises hundreds of cryptically reproducing filamentous species that do not form recognizable mycorrhizal structures and have saprotrophic potential, yet are omnipresent in roots and rhizosphere soil and show ecosystem and host root habitat specificity.
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              Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi

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                Author and article information

                Journal
                MycoKeys
                MycoKeys
                MycoKeys
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2018
                23 February 2018
                : 30
                : 31-39
                Affiliations
                [1 ] Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
                [2 ] Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
                [3 ] Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
                Author notes
                Corresponding author: Martin Ryberg ( martin.ryberg@ 123456ebc.uu.se )

                Academic editor: T. Lumbsch

                Article
                10.3897/mycokeys.30.24376
                5904500
                29681731
                431b12e2-cfc3-47c4-8408-41167b7dfe52
                Martin Ryberg, R. Henrik Nilsson

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 February 2018
                : 13 February 2018
                Funding
                Funded by: Alfred P. Sloan Foundation 100000879 http://doi.org/10.13039/100000879
                Categories
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                taxonomy,nomenclature,mycology,biodiversity
                taxonomy, nomenclature, mycology, biodiversity

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