**1. Introduction**

Large numbers of people in developing countries rely on wild plant species for their medicinal needs. Over thousands of plant species are used in traditional medicine in different parts of the world. During ancient and modern culture, the healing properties of certain plants have been identified, and these plants currently play a significant role in the treatment of various diseases [1]. Due to their medicinal properties, there is a continuous and perpetual interest in researching and utilizing these valuable natural resources, as demonstrated by a plethora of literature (e.g., [2–10]). Different plant species have been used in ethnomedicine in the Arabian Peninsula since ancient times [5,10]. Sakkir [11] provided an overview of the medicinal plants in the United Arab Emirates (UAE) flora and indicated that roughly 18% of the total plant species identified have medicinal values.

**Citation:** Jamdade, R.; Mosa, K.A.; El-Keblawy, A.; Al Shaer, K.; Al Harthi, E.; Al Sallani, M.; Al Jasmi, M.; Gairola, S.; Shabana, H.; Mahmoud, T. DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates. *Diversity* **2022**, *14*, 262. https:// doi.org/10.3390/d14040262

Academic Editors: Morgan Gostel and W. John Kress

Received: 27 January 2022 Accepted: 17 March 2022 Published: 30 March 2022

**Publisher's Note:** MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

These authors attributed such a low representation of medicinal plants in UAE flora to be most likely due to the unknown medicinal properties of the remaining taxa or lack of documentation of their traditional uses. Cybulska et al. [12] reviewed the available information on the medicinal uses of the halophytes in the UAE flora and highlighted the presence of valuable medicinal plants. These medicinally important plants display a specific tolerance to environmental stresses such as high temperature, drought, and salinity. It is expected that these medicinal halophytes might represent a valuable source of phytochemicals in salt marshes, where harsh conditions induce the production of both enzymes and phytochemicals in response to Reactive Oxygen Species (ROS) [12].

A recent survey on the ethnomedicinal knowledge of commonly used medicinal plants in a part of the UAE highlighted the importance of traditional medicinal plants and the need for knowledge documentation [13]. Further, due to various threats to medicinal plants, such as habitat loss and alteration, and overgrazing, there is a need for proper identification and conservation. Phondani et al. [8] documented the ethnobotanical uses of 58 medicinally important plants of the Arabian deserts. They emphasized the need to document ethnobotanical knowledge for sustainability and scientific validation to conserve these valuable medicinal plants native to the Arabian deserts. The above proves the importance of using many UAE plants in folk medicine.

There is a continued increase in the demand for herbal medicinal plants. Therefore, there are some accidental or intentional contaminations and adulteration with nonmedicinal plants or other undesirable plant tissues [14,15]. Such contamination could reduce the effectiveness of the active ingredients, which might lead to detrimental health consequences [16,17]. The authentication of plant material has become necessary for safe use, avoiding adulteration, and trade in medicinal plants. Therefore, there is a need for fast authentication methods to authenticate dried herbal medicinal plants from the other components [18]. The detection of adulteration requires accurate, fast molecular techniques for plant identification, especially if it is difficult to discriminate between closely related plants morphologically [19]. In addition, the proper identification and documentation of medicinal plants in the region could add to their conservation and sustainable utilization.

The classical taxonomic techniques based on morphology and anatomy complement molecular techniques for accurately identifying morphologically similar closely related plant taxa. Currently, there are initiatives for generating DNA barcode libraries of vascular plant flora. Completing such libraries and making them available will help fast, accurate identification, which would lead to the better conservation and utilization of native plants, particularly those used in herbal medicine [20–22]. In this context, a tool such as DNA barcoding could help resolve these issues and lead to the rapid and accurate identification of medicinal species. Moreover, DNA barcoding could be helpful in the identification of medicinal plants in trade, as most herbal material is traded as dried leaves, roots, and bark or in powdered form, thus contributing to their safe use and avoiding adulteration [23].

DNA barcoding has become a useful complementary tool in diverse disciplines of biological sciences. The application of plant DNA barcodes, especially in floristic investigations, ecology, evolution, and conservation fields, has gained momentum over the last decade [24,25]. Several studies have highlighted the potential applications of DNA barcoding in the accurate identification of taxa, discovery of cryptic species, and as an crucial component in phylogenetics investigations [24,26–28]. However, this technique also has some potential limitations, especially in plants where the selected barcode region might lack enough information to provide DNA level species-specific differences and the concurrent observation of such differences at the secondary metabolite level, similar to that observed by Celi ´nski et al. [29].

In medicinal plant research, DNA barcoding is emerging as a valuable molecular identification technique that has greatly ensured the safety and effectiveness of plant materials of medicinal value [30]. The reviews by Techen et al. [31] and Nazar et al. [32] have discussed the selection of the genomic regions as possible barcodes for medicinal plants, including new achievements in the field of DNA barcoding. Those reviews provide

a comprehensive overview of DNA-based methods, technologies, and a combination of three or more genomic regions that were investigated for medicinal plant identification by various researchers worldwide.

Over the years, researchers have suggested different coding and noncoding genes in the nuclear and plastid genomes as potential barcodes for plants [33–37]. The types of DNA barcode markers used for plant identification range from a single chloroplast region to a combination of different regions (see [30,31,38]). Significant progress has been made in the identification of medicinal plants using DNA barcoding (e.g., [25,31,39–47]. For medicinal plant identification, some researchers have used a combination of markers between matK, rbcL, trnH-psbA, and ITS2 sequences. For example, Schori et al. [48] analyzed the rbcL, matK, and psbA-trnH loci of fourteen species of medicinal plants and found that depending on the plant to be identified, one region was preferred over the other, as a single barcode region is not enough to ensure the species identification.

Moreover, along with the selection of efficient DNA barcode markers for species identification, it is necessary to utilize competent methods for effective species discrimination. The results produced by one or more methods sometimes differ, which could require the implementation of more than one method that must be applied and compared jointly [49,50]. The most conventional DNA barcode analysis method is the pairwise distance-based unsupervised Operational Taxonomic Unit (OTU) picking method, where Automated Barcode Gap Discovery (ABGD) is the most widely used tool, followed by the recently developed Assemble Species by Automatic Partitioning (ASAP) [50,51]. Comparatively, some studies have shown a higher rate of species discrimination using the supervised learning approach [21,52–55]. Thus, in this study, we used a comparative approach of implementing both unsupervised and supervised methods for species delimitation.

The UAE has not received much attention to digitally record flora in the form of DNA barcodes [22], as there are only three studies cataloging flora of the UAE to date. Moreover, there are scarce studies on the DNA barcodes of medicinal plants [56], and existing studies have amplified three barcode loci for the coding genes matK, rbcL, and rpoC1 in 10 flowering plants from the UAE. Maloukh et al. [57] focused on authenticating the morphological identification of 51 plant species using rbcL and matK regions. Further, Mosa et al. [15] provided evidence that DNA barcoding was efficient in the detection of adulteration in plant-based herbal products in the UAE. Based on the results obtained, these authors also suggested rbcL as a promising barcode locus for resolving their studied species.

Since 2018, the Sharjah Seed Bank and Herbarium have engaged in the process of DNA barcoding the entire UAE flora [20–22]. Here, we assessed the capability of plastid DNA barcode markers rbcL and matK, and a nuclear marker, ITS2, for the identification of 20 medicinally important plant species belonging to the order Caryophyllales. The core Caryophyllales represent one of the largest eudicot orders with about 12,000 species and 30 families worldwide [58], and some species are used medicinally [59,60]. Various molecular systematic studies on Caryophyllales are available that have substantially increased our knowledge of their phylogeny [61]. The Caryophyllales is represented in the UAE's flora by 11 families. These are Aizoaceae, Amaranthaceae, Caryophyllaceae, Frankeniaceae, Gisekiaceae, Molluginaceae, Nyctaginaceae, Plumbaginaceae, Polygonaceae, Portulacaceae, and Tamaricaceae [62,63]. Among the families of Caryophyllales that have difficulties in morphological discrimination, especially during vegetative stages of the life cycles, are Amaranthaceae (e.g., *Haloxylon persicum*, *H. salicornicum*, *Salicornia persica*), Polygonaceae (e.g., *Calligonum comosum* and *C. crinitum*), and Tamaricaceae (*Tamarix aucheriana* and *T. nilotica*).

The objective of the present study was to barcode the medicinal plant species, compare the discriminatory power of the standard barcode regions, and explore the taxonomic implications in the studied taxa. Establishing a DNA barcoding system could facilitate the conservation of the UAE's medicinal taxa, help overcome the limitations of morphological characters, and contribute to species identification for their efficient utilization. The study results could help generate DNA barcode libraries of the UAE vascular plant flora, which could be a step toward completing the UAE and global DNA barcoding libraries.
