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      Taxonomic revision of the Typhula ishikariensis complex

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          Abstract

          Typhula ishikariensis and the related fungi were separated into three biological species by morphological and physiological characteristics, as well as DNA sequences and mating reactions. We propose that the T. ishikariensis complex should be divided into three species ( T. ishikariensis, T. canadensis and T. hyperborea) and two varieties ( T. ishikariensis var. ishikariensis and var. idahoensis). Typhula hyperborea was reappraised to be recognized also as a separate species of the T. ishikariensis complex.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            R. C. Edgar (2004)
            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              MRBAYES: Bayesian inference of phylogenetic trees.

              J P Huelsenbeck, F Ronquist (2001)
              The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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                Author and article information

                Contributors
                Tamotsu Hoshino: t-hoshino@hi-tech.ac.jp
                Journal
                Journal ID (nlm-ta): Mycoscience
                Journal ID (iso-abbrev): Mycoscience
                Journal ID (publisher-id): mycosci
                Title: Mycoscience
                Publisher: The Mycological Society of Japan (Tokyo, JAPAN )
                ISSN (Print): 1340-3540
                ISSN (Electronic): 1618-2545
                Publication date (Electronic, pub): 31 May 2022
                Publication date (Electronic, collection): 2022
                Volume: 63
                Issue: 3
                Pages: 118-130
                Affiliations
                [a] a Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
                [b] b Present address: Hachinohe Institute of Technology
                [c] c N.V. Tsitsin Main Botanical Garden, Russian Academy of Sciences
                [d] d Graduate School of Life and Environmental Sciences, Osaka Prefecture University
                [e] e Norwegian University of Life Science
                [f] f Department of Biology, Keio University
                [g] g Fellow, National Agriculture and Food Research Organization
                [h] h HOKUREN Agricultural Research Institute
                Author notes
                * Corresponding author. Tel: +81-178-25-8174; fax: +81-178-25-6825 Postal address: Hachinohe Institute of Technology, Obiraki 88-1, Myo, Hachinote, Aomori, 031-8501, Japan. E-mail address: t-hoshino@ 123456hi-tech.ac.jp
                Article
                Publisher-manuscript ID: mycosci.2022.03.003
                DOI: 10.47371/mycosci.2022.03.003
                PMC ID: 10042319
                SO-VID: 6d161e0c-146a-4c32-ab93-4129faf202a2
                Copyright © 2022, by The Mycological Society of Japan
                License:

                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
                Date received : 1 April 2021
                Date revision received : 22 March 2022
                Date accepted : 22 March 2022
                Funding
                Funded by: This research was financially supported in part by a Grant-in-Aid for Scientific Research (KAKENHI) (no. 19570100) from the Japanese Society for the Promotion of Science (JSPS), New Energy and Industrial Technology Development Organization (NEDO) in Japan, Institute for Fermentation, Osaka (IFO) and the Research Council of Norway.
                Categories
                Subject: Short Communication

                Keywords: ecophysiology,pleurotineae (typhulaceae),snow mold,speciation,species complex
                Data availability:
                Keywords: ecophysiology, pleurotineae (typhulaceae), snow mold, speciation, species complex

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