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      DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China

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          Abstract

          The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions ( rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested ( rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.

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          Biodiversity loss and its impact on humanity.

          The most unique feature of Earth is the existence of life, and the most extraordinary feature of life is its diversity. Approximately 9 million types of plants, animals, protists and fungi inhabit the Earth. So, too, do 7 billion people. Two decades ago, at the first Earth Summit, the vast majority of the world's nations declared that human actions were dismantling the Earth's ecosystems, eliminating genes, species and biological traits at an alarming rate. This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper.
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            A DNA barcode for land plants.

            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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              Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

              Background The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Methodology/Principal Findings Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. Conclusions The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                05 December 2016
                2016
                : 7
                : 1791
                Affiliations
                [1] 1Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
                [2] 2College of Life Sciences, University of Chinese Academy of Sciences Beijing, China
                [3] 3Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences Shanghai, China
                [4] 4Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden Shanghai, China
                Author notes

                Edited by: Renchao Zhou, Sun Yat-sen University, China

                Reviewed by: János Taller, University of Pannonia, Hungary; Łukasz Kajtoch, Institute of Systematics and Evolution of Animals (PAN), Poland; Junwen Zhai, College of Landscape Architecture, China

                *Correspondence: Fuwu Xing xinfw@ 123456scib.ac.cn

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2016.01791
                5136562
                27994608
                847e478b-da0c-42fb-9375-c15f1b99a60d
                Copyright © 2016 Li, Tong and Xing.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 23 September 2016
                : 14 November 2016
                Page count
                Figures: 2, Tables: 2, Equations: 0, References: 61, Pages: 9, Words: 6516
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31370231
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                dna barcoding,oberonia,taxonomy,radiation,species identification,its
                Plant science & Botany
                dna barcoding, oberonia, taxonomy, radiation, species identification, its

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