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      DNA barcoding of flowering plants in Sumatra, Indonesia

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          Abstract

          The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land‐use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best‐close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best‐close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two‐loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty‐one species were found to be nonmonophyletic with both markers. The two‐loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.

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          Most cited references 66

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          A DNA barcode for land plants.

            (2009)
          DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
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            SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

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              Use of DNA barcodes to identify flowering plants.

              Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.
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                Author and article information

                Contributors
                fitri.amandita@menlhk.go.id
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                30 January 2019
                February 2019
                : 9
                : 4 ( doiID: 10.1002/ece3.2019.9.issue-4 )
                : 1858-1868
                Affiliations
                [ 1 ] Department of Forest Genetics and Forest Tree Breeding Georg‐August University Göttingen Germany
                [ 2 ] Research and Development Center for Environmental Quality and Laboratory
                [ 3 ] Biodiversity, Macroecology, and Biogeography Research Group Georg‐August University Göttingen Germany
                [ 4 ] Botanical Garden of the University of Bern Bern Switzerland
                [ 5 ] Bogor Botanical Garden Lembaga Ilmu Pengetahuan Indonesia Bogor Indonesia
                [ 6 ] Department of Silviculture Bogor Agricultural University (IPB) Bogor Indonesia
                [ 7 ] University of Kassel Kassel Germany
                Author notes
                [* ] Correspondence

                Fitri Yola Amandita, Ministry of Environment and Forestry, Research and Development Center for Environmental Quality and Laboratory, Tangerang Selatan, Indonesia.

                Email: fitri.amandita@ 123456menlhk.go.id

                Article
                ECE34875
                10.1002/ece3.4875
                6392390
                © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 2, Tables: 2, Pages: 11, Words: 24181
                Product
                Funding
                Funded by: Deutsche Forschungsgemeinschaft
                Award ID: EFForTS project
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece34875
                February 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.0 mode:remove_FC converted:27.02.2019

                Evolutionary Biology

                dna marker, efforts project, matk, molecular identification, rbcl, sumatra

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