Special Issue "Plant DNA Barcode"

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: 30 September 2019.

Special Issue Editor

Guest Editor
Dr. Maria (Masha) Kuzmina Website E-Mail
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 1200 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 (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:

Research

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
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)
Show Figures

Figure 1

Back to TopTop