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      Taxonomy and phylogeny of Exobasidium pentasporium causing witches' broom of Rhododendron species

      research-article
      a , a , *
      Mycoscience
      The Mycological Society of Japan
      epitypification, Exobasidiaceae, Exobasidiales, plant pathogen

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          Abstract

          Exobasidium pentasporium was first found on Rhododendron kaempferi in Nikko, Tochigi Prefecture, Japan and described only with a brief mentions and illustration of a specimen in 1896. This fungus causes a witches' broom disease of Rhododendron species. To stabilize the concept of this species, the specimen in the protologue was located, carefully examined, and illustrated. In addition, the name was epitypified based on a newly collected topotype specimen. A phylogenetic tree using ITS and LSU sequences showed that our isolates of E. pentasporium grouped with other Exobasidium species on Rhododendron forming a monophyletic clade with strong statistical support and were unrelated to E. nobeyamense , another causal agent of witches' broom disease on Rhododendron species.

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          Most cited references23

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            A new look at the statistical model identification

            IEEE Transactions on Automatic Control, 19(6), 716-723
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              RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

              Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng . RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/ . Supplementary information Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                yuurihirooka@hosei.ac.jp
                Journal
                Mycoscience
                Mycoscience
                mycosci
                Mycoscience
                The Mycological Society of Japan (Tokyo, JAPAN )
                1340-3540
                1618-2545
                20 September 2022
                2022
                : 63
                : 6
                : 247-253
                Affiliations
                [a] a Department of Clinical Plant Science, Faculty of Bioscience, Hosei University
                Author notes
                * Corresponding author. Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan E-mail address: yuurihirooka@ 123456hosei.ac.jp (Y. Hirooka).
                Article
                mycosci.2022.07.002
                10.47371/mycosci.2022.07.002
                10042312
                29d0f57e-9235-4272-b2f7-bfd995bcd26a
                2021, by The Mycological Society of Japan

                This is an open-access paper distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivative 4.0 international license (CC BY-NC-ND 4.0: https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 16 February 2022
                : 2 July 2022
                : 17 July 2022
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                epitypification,exobasidiaceae,exobasidiales,plant pathogen

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