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      Taxonomic revision of Russula subsection Amoeninae from South Korea

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          Russula subsection Amoeninae is morphologically defined by a dry velvety pileus surface, a complete absence of cystidia with heteromorphous contents in all tissues, and spores without amyloid suprahilar spot. Thirty-four species within subsection Amoeninae have been published worldwide. Although most Russula species in South Korea have been assigned European or North American names, recent molecular studies have shown that Russula species from different continents are not conspecific. Therefore, the present study aims to: 1) define which species of Russula subsection Amoeninae occur on each continent using molecular phylogenetic analyses; 2) revise the taxonomy of Korean Amoeninae . The phylogenetic analyses using the internal transcribed spacer (ITS) and multilocus sequences showed that subsection Amoeninae is monophyletic within subgenus Heterophyllidiae section Heterophyllae . A total of 21 Russula subsection Amoeninae species were confirmed from Asia, Australia, Europe, North America, and Central America, and species from different continents formed separate clades. Three species were recognized from South Korea and were clearly separated from the European and North American species. These species are R. bella , also reported from Japan, a new species described herein, Russula orientipurpurea , and a new species undescribed due to insufficient material.

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          Most cited references 73

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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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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

                Author and article information

                Pensoft Publishers
                09 November 2020
                : 75
                : 1-29
                [1 ] School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea Seoul National University Seoul South Korea
                [2 ] National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Klong Luang, Pathum Thani 12120, Thailand National Biobank of Thailand Pathum Thani Thailand
                [3 ] Department of Botany & Microbiology, H.N.B. Garhwal University (A Central University), Srinagar, Garhwal, 246174, Uttarakhand, India Korea National Arboretum Pocheon South Korea
                [4 ] A.J.C. Bose Indian Botanic Garden, Botanical Survey of India, P.O. Botanic Garden, Howrah 711103, India Garhwal University Srinagar India
                [5 ] ISYEB (CNRS, Sorbonne Université, EPHE) Institut de Systématique, Évolution, Biodiversité, Muséum national d’Histoire naturelle, case postale 39, 57 rue Cuvier, F-75231 Paris cedex 05, France A.J.C. Bose Indian Botanic Garden Howrah India
                [6 ] Department of Biology, Duke University, Durham, NC 27708, USA Muséum national d’Histoire naturelle Paris France
                [7 ] Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia Duke University Durham United States of America
                [8 ] Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, South Korea Slovak Academy of Sciences Bratislava Slovakia
                [9 ] Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, South Korea National Institute of Biological Resources Incheon South Korea
                Author notes
                Corresponding author: Young Woon Lim ( ywlim@ 123456snu.ac.kr )

                Academic editor: Zai-Wei Ge

                Komsit Wisitrassameewong, Myung Soo Park, Hyun Lee, Aniket Ghosh, Kanad Das, Bart Buyck, Brian P. Looney, Miroslav Caboň, Slavomír Adamčík, Changmu Kim, Chang Sun Kim, Young Woon Lim

                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.

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