Special Issue "Plant DNA Barcode"

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 January 2020).

Special Issue Editor

Dr. Maria (Masha) Kuzmina
Website
Guest Editor
Center for Biodiversity Genomics, University of Guelph, Guelph, Ontario N1G 1P4, Canada
Interests: plant DNA barcoding; forensic and ecological applications of DNA barcoding; biogeography; systematics of vascular plants

Special Issue Information

Dear colleagues,

In 2003, DNA barcoding was defined as a method of species identification using a short section of DNA from a standardized region of the genome. The 5’ region of the mitochondrial cytochrome c oxidase I (COI) gene, although being an ideal DNA barcode for animals, was not a good candidate for plants due to extremely low rates of nucleotide substitution in mitochondrial genes in most plant lineages. As such, plant DNA barcoding launched only in 2009 when the core of two DNA regions from the chloroplast, RuBisCO large subunit (rbcL), and group II intron maturase (matK) genes were accepted by CBOL Plant Working Group for land plants. Since the adoption of the loci to be used in plant DNA barcode work, intense research has focused on their effectiveness, integration with High Throughput Sequencing (HTS) methods, and application to a wide range of basic and applied research. A summary search of the keywords “plant barcode” showed over 1,200 publications devoted to the subject in the last decade. The subjects covered are hugely diverse, and include biodiversity surveys, taxonomic revisions, and ecological and agricultural applications to the area of metagenomics.

A number of review papers have reflected the dramatic transformation of the application of plant DNA barcoding in these ten years since its adoption. Tens of thousands new, often unique, plant sequencing records were deposited in the GenBank and Barcode of Life Data management systems (BOLD). This pool became an unparalleled resource of the references for a variety of interesting applications, e.g., the authentication of food supplements, dietary analysis and reconstruction of the plant–herbivore networks, pollination, environmental (eDNA) and ancient (aDNA) DNA analyses, as well as wild-life conservation. A variety of studies used plant DNA barcodes to explore comparative community phylogenies, biogeography, and systematics. Extensive interactions of researchers using DNA barcode data with taxonomists compiling natural history collections, opened the discussion about the regulations of collaboration, the obligations of researchers under the Nagoya Protocol, and how we can and must share novel genetic data. Further, the wave of data that has been generated by DNA barcoding studies, particularly in the era of HTS, has pushed DNA barcoding into the arena of metagenomics (or metabarcoding), which itself has led to a need for exploring new analytical methods for analysis. Lastly, some research efforts have continued to push the boundary of what a DNA barcode is, toward the use of the complete plastome, or even whole genome shotgun sequencing data. Clearly, DNA barcoding serves a vital role in many areas of research. A Special Issue that helps summarize the progress made, promising developments, and areas for further exploration is well due.

This Special Issue encourages the authors to submit their original research papers, methods, perspectives, opinions, and reviews related to the different aspects of plant DNA barcoding: building the reference library of life, whole plastome and total genome sequencing, biosystematics, metabarcoding, eDNA, aDNA, dietary analysis, food webs, pollination, the authentication of food and food supplements, conservation, community phylogenetic, ecology and evolution, and the international rules and regulations for sequencing data sharing.

Dr. Maria (Masha) Kuzmina
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Reference DNA library
  • Metabarcoding
  • High throughput sequencing
  • Plastome
  • Whole genome shotgun sequencing
  • Environmental DNA
  • Ancient DNA
  • Dietary
  • Food webs
  • Pollination
  • Plant supplements
  • Food authentication
  • Conservation
  • Invasive species
  • Community phylogenetic
  • Biogeography
  • Biosystematics
  • Ecology
  • Evolution
  • Herbarium
  • Nagoya protocol
  • Genetic data sharing

Published Papers (6 papers)

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Research

Open AccessArticle
Applied Barcoding: The Practicalities of DNA Testing for Herbals
Plants 2020, 9(9), 1150; https://doi.org/10.3390/plants9091150 - 04 Sep 2020
Cited by 1
Abstract
DNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation of DNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change [...] Read more.
DNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation of DNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change in status, requiring the establishment of standardized, reliable and reproducible methods. The process by which this can be achieved for any herbal medicine is described, using Hypericum perforatum L. (St John’s Wort) and potential adulterant Hypericum species as a case study. A range of practical issues are considered including quality control of DNA sequences from public repositories and the construction of individual curated databases, choice of DNA barcode region(s) and the identification of informative polymorphic nucleotide sequences. A decision tree informs the structure of the manuscript and provides a template to guide the development of future DNA barcode tests for herbals. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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Open AccessArticle
Molecular Verification of the UK National Collection of Cultivated Liriope and Ophiopogon Plants
Plants 2020, 9(5), 558; https://doi.org/10.3390/plants9050558 - 27 Apr 2020
Abstract
A collection of cultivated Liriope and Ophiopogon plants was established in 1996–1998 and subsequently hosted at a horticultural college. Uncertainties about the identification of the accessions, compounded by potential errors in propagation and labelling have led to waning confidence in the identities of [...] Read more.
A collection of cultivated Liriope and Ophiopogon plants was established in 1996–1998 and subsequently hosted at a horticultural college. Uncertainties about the identification of the accessions, compounded by potential errors in propagation and labelling have led to waning confidence in the identities of the plants in the collection. The potential for using DNA barcoding to determine the species identities of the accessions was investigated. The DNA barcode regions of the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene (rbcL) and nuclear ribosomal internal transcribed spacer (nrITS) were amplified. DNA sequence analysis allowed the sequences of the accessions to be compared to reference sequences in public databases. A simple haplotype map of the characteristic polymorphic positions in the rbcL regions was used to clearly distinguish between the two genera and assign Ophiopogon accessions to individual species or sub-groups of species. The ITS sequence data confirmed these genus and species assignations and provided greater resolution to distinguish between closely related species. The combination of two DNA barcodes allowed most of the accessions to be assigned to individual species. This molecular verification confirmed the identity of about 70% of the accessions, with the remaining 30% demonstrating a range of mistaken identities at the species and genus levels. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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Open AccessArticle
The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
Plants 2020, 9(4), 432; https://doi.org/10.3390/plants9040432 - 01 Apr 2020
Cited by 3
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 [...] Read more.
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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Open AccessArticle
First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales)
Plants 2020, 9(2), 284; https://doi.org/10.3390/plants9020284 - 21 Feb 2020
Cited by 1
Abstract
Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are [...] Read more.
Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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Open AccessArticle
Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra
Plants 2019, 8(11), 461; https://doi.org/10.3390/plants8110461 - 30 Oct 2019
Cited by 3
Abstract
DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, [...] Read more.
DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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Open AccessArticle
Distribution and Community Assembly of Trees Along an Andean Elevational Gradient
Plants 2019, 8(9), 326; https://doi.org/10.3390/plants8090326 - 05 Sep 2019
Cited by 1
Abstract
Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated [...] Read more.
Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440–3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon–Weaver diversity, Simpson’s Dominance, Simpson’s Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations. Full article
(This article belongs to the Special Issue Plant DNA Barcode)
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