Plant DNA Barcode

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

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