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      Diversity of Trametes (Polyporales, Basidiomycota) in tropical Benin and description of new species Trametes parvispora

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          Abstract

          Abstract

          Trametes is a globally distributed genus of white-rot polypores and well sampled in temperate and boreal areas. However, the diversity, taxonomy, and phylogenetic positions of Trametes spp. are poorly known in tropical Africa. This study aims at documenting the diversity of Trametes species in Benin (tropical Africa) and their phylogenetic positions with a focus on the T. elegans species complex. Therefore, we collected specimens of Trametes from different forest types across Benin. To infer phylogenetic relationships between Trametes species, we investigated sequences of five gene regions and added available sequences from GenBank. Using Maximum likelihood and Bayesian phylogeny inference methods, we found eight supported species clades. For the T. elegans species complex, we re-establish the name Trametes palisotii for species previously known as T. elegans in tropical Africa. Furthermore, we propose Trametes parvispora as a species new to science and provide the description of this species. Our molecular phylogeny of Trametes with a focus on tropical Benin contributes to taxonomic clarity of an important wood-decay fungal genus, which is the basis for biodiversity assessments of Trametes in the tropics.

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          Most cited references34

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          GenBank

          GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.
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            Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales).

            P. Matheny (2005)
            Approximately 3000 bp across 84 taxa have been analyzed for variable regions of RPB1, RPB2, and nLSU-rDNA to infer phylogenetic relationships in the large ectomycorrhizal mushroom genus Inocybe (Agaricales; Basidiomycota). This study represents the first effort to combine variable regions of RPB1 and RPB2 with nLSU-rDNA for low-level phylogenetic studies in mushroom-forming fungi. Combination of the three loci increases non-parametric bootstrap support, Bayesian posterior probabilities, and resolution for numerous clades compared to separate gene analyses. These data suggest the evolution of at least five major lineages in Inocybe-the Inocybe clade, the Mallocybe clade, the Auritella clade, the Inosperma clade, and the Pseudosperma clade. Additionally, many clades nested within each major lineage are strongly supported. These results also suggest the family Crepiodataceae sensu stricto is sister to Inocybe. Recognition of Inocybe at the family level, the Inocybaceae, is recommended.
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              Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales).

              An investigation of mushroom phylogeny using the largest subunit of RNA polymerase II gene sequences (RPB1) was conducted in comparison with nuclear ribosomal large subunit RNA gene sequences (nLSU) for the same set of taxa in the genus Inocybe (Agaricales, Basidiomycota). The two data sets, though not significantly incongruent, exhibit conflict among the placement of two taxa that exhibit long branches in the nLSU data set. In contrast, RPB1 terminal branch lengths are rather uniform. Bootstrap support is increased for clades in RPB1. Combined data sets increase the degree of confidence for several relationships. Overall, nLSU data do not yield a robust phylogeny when independently assessed by RPB1 sequences. This multigene study indicates that Inocybe is a monophyletic group composed of at least four distinct lineages-subgenus Mallocybe, section Cervicolores, section Rimosae, and subgenus Inocybe sensu Kühner, Kuyper, non Singer. Within subgenus Inocybe, two additional lineages, one composed of species with smooth basidiospores (clade I) and a second characterized by nodulose-spored species (clade II), are recovered by RPB1 and combined data. The nLSU data recover only clade I. The genera Astrosporina and Inocybella cannot be recognized phylogenetically. "Supersections" Cortinatae and Marginatae are not monophyletic groups.
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                Author and article information

                Contributors
                Journal
                MycoKeys
                MycoKeys
                11
                urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2020
                10 March 2020
                : 65
                : 25-47
                Affiliations
                [1 ] Department of Ecology, Universität Kassel, Heinrich-Plett-Str. 40, Kassel, Germany
                [2 ] Research Unit Tropical Mycology and Plant-Soil Fungi Interactions (MyTIPS), University of Parakou BP 123, Parakou, Benin
                [3 ] Laboratory of Applied Ecology, University of Abomey-Calavi (LEA/UAC), Benin
                [4 ] Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
                [5 ] Bavarian Forest National Park, Freyunger Str. 2, 94481 Grafenau, Germany
                [6 ] Department of Mycology, Biologicum, Goethe Universität, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
                Author notes
                Corresponding author: Boris Armel Olou ( borisolou@ 123456yahoo.fr )

                Academic editor: M.-A. Neves

                Author information
                https://orcid.org/0000-0002-3629-5360
                https://orcid.org/0000-0001-7866-7508
                https://orcid.org/0000-0002-7043-5769
                Article
                47574
                10.3897/mycokeys.65.47574
                7078339
                32206024
                5543297d-1a8d-46bf-9590-8197313cd681
                Boris Armel Olou, Franz-Sebastian Krah, Meike Piepenbring, Nourou Soulemane Yorou, 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
                : 28 October 2019
                : 22 December 2019
                Categories
                Research Article
                Agaricomycetes
                Polyporales
                Molecular Systematics
                Phylogeny
                Taxonomy
                West Africa

                africa,morphology,new taxa,phylogeny, polyporales ,taxonomy,tropics,white rot,fungi,polyporales,polyporaceae

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