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      A new synonym of Polygonatum in China, based on morphological and molecular evidence

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          Abstract

          Polygonatum kingianum Collett et Hemsl. var. grandifolium D.M. Liu & W.Z. Zeng (1981), which sprouts twice a year, once in spring and once in autumn, differs from Polygonatum kingianum in leaves, bracts, perianth and filaments. Morphological comparison and molecular phylogeny indicate that it is identical to the newly-published Polygonatum hunanense H.H. Liu & B.Z. Wang (2021). Hence, we propose that P. kingianum var. grandifolium should be recognised as a new synonym of P. hunanense . In addition, phylogenetic analyses confirmed that P. hunanense is sister to Polygonatum sect. Polygonatum , rather than P. kingianum of Polygonatum sect. Verticillata .

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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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            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.
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              jModelTest 2: more models, new heuristics and parallel computing.

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                Author and article information

                Contributors
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2021
                12 April 2021
                : 175
                : 137-149
                Affiliations
                [1 ] Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China Zhejiang University Hangzhou China
                [2 ] State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, China Zhejiang A&F University Hangzhou China
                Author notes

                Academic editor: L. Peruzzi

                Author information
                https://orcid.org/0000-0002-9407-7740
                Article
                63383
                10.3897/phytokeys.175.63383
                8390792
                34475796
                e4035131-b034-4573-bbd2-4131b9b779ce
                Maoqin Xia, Ying Liu, Jingjing Liu, Donghong Chen, Yan Shi, Zhicong Bai, Yu Xiao, Chen Peng, Jinping Si, Pan Li, Yingxiong Qiu

                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
                : 20 January 2021
                : 22 March 2021
                Funding
                Funded by: Zhejiang A and F University 501100008827 http://doi.org/10.13039/501100008827
                Categories
                Research Article
                Asparagaceae
                Taxonomy
                China

                Plant science & Botany
                polygonatum hunanense , polygonatum kingianum var. grandifolium ,phylogeny,plastome

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