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      DNA Barcoding of Andaliman ( Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia Using Maturase K Gene

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          Abstract

          Andaliman ( Zanthoxylum acanthopodium DC) is a native plant of North Sumatra province. Zanthoxylum acanthopodium is a member of Rutaceae family widely found in northern Sumatra, Indonesia. The aim of this study was to barcode Z. acanthopodium in North Sumatra province, Indonesia based on cpDNA maturase K ( matK). Samples were collected in seven localities across six regions of North Sumatra province. Phylogenetic analysis was conducted using Maximum Likelihood method. The results of phylogenetic analysis indicate that Z. acanthopodium is a monophyletic group that is derived from a common ancestor. The results of the phylogenetic tree construction show that there is a grouping of accession between Z. acanthopodium species separate from other species in the Zanthoxylum genus as well as those of the Rutaceae family. The results showed that cpDNA matK marker can effectively be used as DNA barcoding to identify Z. acanthopodium.

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          Most cited references 43

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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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            Universal primers for amplification of three non-coding regions of chloroplast DNA.

            Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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              A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

              Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.
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                Author and article information

                Journal
                Trop Life Sci Res
                Trop Life Sci Res
                Tropical Life Sciences Research
                Tropical Life Sciences Research
                Penerbit Universiti Sains Malaysia
                1985-3718
                2180-4249
                June 2021
                29 June 2021
                : 32
                : 2
                : 15-28
                Affiliations
                [1 ]Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
                [2 ]Department of Biology, Faculty of Sciences and Technology, Islamic University of Assyafiiyah, Jl. Jatiwaringin Raya, No 12, East Jakarta,17411 Indonesia
                [3 ]Department of Biology, Faculty of Sciences and Technology, Islamic State University Sunan Ampel Surabaya, Jl. Ahmad Yani 117 Surabaya, East Java, 60237, Indonesia
                Author notes
                [* ]Corresponding author: ekoprasetya.biologi@ 123456gmail.com
                Article
                tlsr-32-2-15
                10.21315/tlsr2021.32.2.2
                8300946
                34367512
                cd19e06b-3d6f-470c-96b6-203b9c371dbb
                © Penerbit Universiti Sains Malaysia, 2021

                This work is licensed under the terms of the Creative Commons Attribution (CC BY) ( http://creativecommons.org/licenses/by/4.0/).

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                Article

                z. acanthopodium, maturase k, north sumatra, dna barcoding

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