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      Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae

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          Mazus lanceifolius ( Mazaceae ) is a perennial herb with opposite leaves and endemic to central China that has not been collected for 130 years. Rediscovery of this enigmatic species in the wild allows for determination of its phylogenetic position within Mazaceae . Phylogenetic reconstruction of Mazaceae based on DNA sequences from four plastid markers ( matK, rbcL, rps16 and trnL- trnF) and nuclear ribosome ITS consistently showed that Mazus was not monophyletic. Mazus lanceifolius is in the most basal clade within Mazaceae , as sister to the remaining species of three recognized genera Dodartia , Lancea and Mazus . These results support the separation of M. lanceifolius from Mazus as a new genus, which was established here as Puchiumazus Bo Li, D.G. Zhang & C.L. Xiang. Meanwhile, a collection from Shennongjia Forestry District of Hubei Province, China, misidentified as “ M. lanceifolius ” in previous molecular study, is here revealed to represent an undescribed species of Mazus , i.e., M. fruticosus Bo Li, D.G. Zhang & C.L. Xiang, sp. nov. Morphologically, Puchiumazus is clearly distinct from the other three genera by having quadrangular to somewhat ribbed stems, and obviously opposite leaves. In addition, we provide a taxonomic key to the four genera of Mazaceae .

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          Most cited references 55

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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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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

             Robert 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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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com

                Author and article information

                Pensoft Publishers
                06 January 2021
                : 171
                : 1-24
                [1 ] CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
                [2 ] Sichuan Academy of Forestry, Chengdu 610081, Sichuan, China Sichuan Academy of Forestry Chengdu China
                [3 ] Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China Jiangxi Agricultural University Nanchang China
                [4 ] Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, China Jishou University Jishou China
                [5 ] State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China Institute of Botany, Chinese Academy of Sciences Beijing China
                [6 ] Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China Sino-African Joint Research Center, Chinese Academy of Sciences Wuhan China
                Author notes
                Corresponding author: Bo Li ( hanbolijx@ 123456163.com )

                Academic editor: A. Paton

                Chun-Lei Xiang, Hong-Li Pan, Dao-Zhang Min, Dai-Gui Zhang, Fei Zhao, Bing Liu, Bo Li

                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.

                Research Article

                Plant science & Botany

                puchiumazus , dodartia , new genus, lancea , lamiales


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