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      Does Calypogeia azurea (Calypogeiaceae, Marchantiophyta) occur outside Europe? Molecular and morphological evidence

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          Abstract

          Oil bodies are the unique feature of most liverworts. Their shape, color and distribution pattern in leaf and underleaf cells are important taxonomic features of the genus Calypogeia. Most species of the genus Calypogeia have pellucid and colorless oil bodies, whereas colored, including gray to pale brown, purple-brown or blue oil bodies, are rare. To date, C. azurea was the only species with blue oil bodies to have been considered as a species of the Holarctic range. This species has been noted in various parts of the northern hemisphere–from North America, through Europe to the Far East. The aim of this study was to determine the genetic diversity of C. azurea from different parts of its distribution range and to ascertain whether blue oil bodies appeared once or several times in the evolution of the genus Calypogeia. The phylogenetic analyses based on four plastid regions ( rbcL, trnG, trnL, trnH-psbA) and one nuclear region (ITS2) revealed that C. azurea is presently a paraphyletic taxon, with other Calypogeia species nested among C. azurea accessions that were clustered into four different clades. Based on the level of genetic divergence (1.03–2.17%) and the observed morphological, ecological and geographical differences, the evaluated clades could be regarded as previously unrecognized species. Four species were identified: C. azurea Stotler & Crotz (a European species corresponding to the holotype), two new species from Pacific Asia— C. orientalis Buczkowska & Bakalin and C. sinensis Bakalin & Buczkowska, and a North American species which, due to the lack of identifiable morphological features, must be regarded as the cryptic species of C. azurea with a provisional name of C. azurea species NA.

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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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            TESTING SIGNIFICANCE OF INCONGRUENCE

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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

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing – original draft
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draft
                Role: Funding acquisitionRole: InvestigationRole: Resources
                Role: MethodologyRole: ResourcesRole: Writing – original draft
                Role: Investigation
                Role: Investigation
                Role: InvestigationRole: Methodology
                Role: Funding acquisitionRole: Methodology
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 October 2018
                2018
                : 13
                : 10
                : e0204561
                Affiliations
                [1 ] Department of Genetics, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
                [2 ] Botanical Garden-Institute, Russian Academy of Science, Vladivostok, Russia
                [3 ] Duke Herbarium, Department of Biology, Duke University, Durham, NC, United States of America
                [4 ] Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
                Universita degli Studi del Piemonte Orientale Amedeo Avogadro, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-1491-8157
                http://orcid.org/0000-0001-7897-4305
                Article
                PONE-D-18-15732
                10.1371/journal.pone.0204561
                6179228
                30304042
                da326b20-c08a-47b6-801a-87f82002c2fd
                © 2018 Buczkowska et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 25 May 2018
                : 30 August 2018
                Page count
                Figures: 8, Tables: 3, Pages: 27
                Funding
                Funded by: Polish National Science Centre
                Award ID: N303 344235
                Award Recipient :
                Funded by: Polish National Science Centre
                Award ID: 2015/19/B/NZ8/03970
                Award Recipient :
                Funded by: Russian Foundation for Basic Researches
                Award ID: 17-04-0018
                Award Recipient :
                Funded by: Vietnam Academy of Science and Technology and the Far Eastern Branch of the Russian Academy of Sciences
                Award ID: ВАНТ17-002
                Award Recipient :
                Funded by: Vietnam Academy of Science and Technology and the Far Eastern Branch of the Russian Academy of Sciences
                Award ID: VAST.HTQT.NGA.02/17-18
                Award Recipient :
                Funded by: Russian Foundation for Basic Researches and Chinese Foundation for Natural Sciences
                Award ID: 12-04-91150
                Award Recipient :
                The work of KB, AB, PG, MŚ, MS, JS was supported by the Polish National Science Centre ( https://www.ncn.gov.pl/), grants no. N303 344235 and 2015/19/B/NZ8/03970. The work of VB was partly supported by the Russian Foundation for Basic Researches no. 17-04-0018 and the collaborative project between the Vietnam Academy of Science and Technology and the Far Eastern Branch of the Russian Academy of Sciences no. ВАНТ17-002 and VAST.HTQT.NGA.02/17-18. The collection of the material in China was accomplished in the course of joint investigation within collaboration project sponsored by the Russian Foundation for Basic Researches (project no. 12-04-91150) and Chinese Foundation for Natural Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Lipids
                Oils
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Research and analysis methods
                Database and informatics methods
                Bioinformatics
                Sequence analysis
                DNA sequence analysis
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                Cell Biology
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