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      Chemotaxonomic Monitoring of Genetically Authenticated Amomi Fructus Using High-Performance Liquid Chromatography–Diode Array Detector with Chemometric Analysis

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          Abstract

          Amomi Fructus is widely used to treat digestive disorders, and Amomum villosum, A. villosum var. xanthioides, and A. longiligulare are permitted medicinally in national pharmacopeias. However, there are a variety of adulterants present in herbal markets owing to their morphological similarities to the genuine Amomum species. Forty-two Amomi Fructus samples from various origins were identified using internal transcribed spacer and chloroplast barcoding analyses, and then their chromatographic profiles were compared using chemometric analysis for chemotaxonomic monitoring. Among the Amomi Fructus samples, A. villosum, A. longiligulare, A. ghaticum, and A. microcarpum were confirmed as single Amomum species, whereas a mixture of either these Amomum species or with another Amomum species was observed in 15 samples. Chemotaxonomic monitoring results demonstrated that two medicinal Amomum samples, A. villosum and A. longiligulare, were not clearly distinguished from each other, but were apparently separated from other non-medicinal Amomum adulterants. A. ghaticum and A. microcarpum samples were also chemically different from other samples and formed their own species groups. Amomum species mixtures showed diverse variations of chemical correlations according to constituent Amomum species. Genetic authentication-based chemotaxonomic monitoring methods are helpful in classifying Amomi Fructus samples by their original species and to distinguish genuine Amomum species from the adulterants.

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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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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

              PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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                Author and article information

                Journal
                Molecules
                Molecules
                molecules
                Molecules
                MDPI
                1420-3049
                07 October 2020
                October 2020
                : 25
                : 19
                : 4581
                Affiliations
                [1 ]Research Center of Traditional Korean Medicine, Wonkwang University, Iksan 54538, Korea; bluemoonlion@ 123456wku.ac.kr
                [2 ]Department of Herbology, College of Korean Medicine, Wonkwang University, Iksan 54538, Korea; rasfin@ 123456wku.ac.kr
                [3 ]Department of Diagnostics, College of Korean Medicine, Wonkwang University, Iksan 54538, Korea; kendu@ 123456wku.ac.kr
                [4 ]Department of Korean Medicinal Physiology, College of Korean Medicine, Wonkwang University, Iksan 54538, Korea; desson@ 123456wku.ac.kr
                [5 ]Division of Pharmacology, School of Korean Medicine, Pusan National University, Yangsan 50612, Korea
                Author notes
                [* ]Correspondence: kmsct@ 123456pusan.ac.kr ; Tel.: +82-51-510-8456
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0003-1479-4991
                https://orcid.org/0000-0003-2049-6640
                https://orcid.org/0000-0002-5836-1963
                https://orcid.org/0000-0002-9704-0206
                Article
                molecules-25-04581
                10.3390/molecules25194581
                7583901
                33036491
                c645a37c-a96f-4ad1-8809-2c731811448d
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 11 September 2020
                : 06 October 2020
                Categories
                Article

                amomi fructus,phylogenetic identification,hplc chromatographic profiling,chemometric analysis,chemotaxonomic monitoring

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