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      Short-spored Subulicystidium (Trechisporales, Basidiomycota): high morphological diversity and only partly clear species boundaries

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          Abstract

          Abstract

          Diversity of corticioid fungi (resupinate Basidiomycota ), especially outside the northern temperate climatic zone, remains poorly explored. Furthermore, most of the known species are delimited by morphological concepts only and, not rarely, these concepts are too broad and need to be tested by molecular tools. For many decades, the delimitation of species in the genus Subulicystidium ( Hydnodontaceae , Trechisporales ) was a challenge for mycologists. The presence of numerous transitional forms as to basidiospore size and shape hindered species delimitation and almost no data on molecular diversity have been available. In this study, an extensive set of 144 Subulicystidium specimens from Paleo- and Neotropics was examined. Forty-nine sequences of ITS nuclear ribosomal DNA region and 51 sequences of 28S nuclear ribosomal DNA region from fruit bodies of Subulicystidium were obtained and analysed within the barcoding gap framework and with phylogenetic Bayesian and Maximum likelihood approaches. Eleven new species of Subulicystidium are described based on morphology and molecular analyses: Subulicystidium boidinii , S. fusisporum , S. grandisporum , S. harpagum , S. inornatum , S. oberwinkleri , S. parvisporum , S. rarocrystallinum , S. robustius , S. ryvardenii and S. tedersooi . Morphological and DNA-evidenced borders were revised for the five previously known species: S. naviculatum , S. nikau , S. obtusisporum , S. brachysporum and S. meridense . Species-level variation in basidiospore size and shape was estimated based on systematic measurements of 2840 spores from 67 sequenced specimens. An updated identification key to all known species of Subulicystidium is provided.

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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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            Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

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              Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.

              Spider: SPecies IDentity and Evolution in R is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation. Included are functions essential for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, and for testing and optimizing divergence threshold limits. In terms of investigating evolutionary and taxonomic questions, techniques for assessing diagnostic nucleotides and probability of reciprocal monophyly are also provided. Additionally, a sliding window function offers opportunities to analyse information across a gene, essential for marker design in degraded DNA studies. Spider capitalizes on R's extensible ethos and offers an integrated platform ideal for the analysis of both nucleotide and morphological data. The program can be obtained from the comprehensive R archive network (CRAN, http://cran.r-project.org) and from the R-Forge package development site (http://spider.r-forge.r-project.org/). © 2012 Blackwell Publishing Ltd.
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                Author and article information

                Journal
                MycoKeys
                MycoKeys
                MycoKeys
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2018
                27 June 2018
                : 35
                : 41-99
                Affiliations
                [1 ] Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
                [2 ] Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
                Author notes
                Corresponding author: Alexander Ordynets ( a.ordynets@ 123456uni-kassel.de )

                Academic editor: M.P. Martín

                Article
                10.3897/mycokeys.35.25678
                6031700
                88d27479-137f-4684-8e31-bb022046d233
                Alexander Ordynets, David Scherf, Felix Pansegrau, Jonathan Denecke, Ludmila Lysenko, Karl-Henrik Larsson, Ewald Langer

                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
                : 10 April 2018
                : 31 May 2018
                Categories
                Research Article
                Agaricomycetes
                Basidiomycota
                Hydnodontaceae
                Trechisporales
                Biogeography
                Bioinformatics
                Catalogues and Checklists
                Data analysis & Modelling
                Data Management
                DNA barcoding
                Identification key
                Microscopy and Spectroscopy
                Molecular systematics
                Nomenclature
                Phylogeny
                Species Inventories
                Taxonomy
                Africa
                Americas
                Asia
                Australasia
                Europe
                Oceans
                Pacific
                World

                basidiospores,biodiversity,biometry,crystals,cystidia,dna barcode,encrustation,genetic distance,internal transcribed spacer,large subunit,species delimitation,taxonomy,fungi,trechisporales,hydnodontaceae

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