Development of genetic markers for Ochradenus arabicus (Resedaceae), an endemic medicinal plant of Saudi Arabia

Effect of Green Synthesized ZnO-NPs on Growth, Antioxidant System Response and Bioactive Compound Accumulation in Echinops macrochaetus, a Potential Medicinal Plant, and Assessment of Genome Size (2C DNA Content)

Echinops macrochaetus is a medicinal plant that can be used to cure various diseases. In the present study, plant-mediated zinc oxide nanoparticles (ZnO-NPs) were synthesized using an aqueous leaf extract of the medicinal plant Heliotropium bacciferum and characterized using various techniques. E. macrochaetus was collected from the wild and identified using the internal transcribed spacer sequence of nrDNA (ITS-nrDNA), which showed the closeness to its related genus in a phylogenetic tree. The effect of synthesized biogenic ZnO-NPs was studied on E. macrochaetus in a growth chamber for growth, bioactive compound enhancement and antioxidant system response. The irrigation of plants at a low concentration of ZnO-NPs (T1 = 10 mg/L) induced more growth in terms of biomass, chlorophyll content (273.11 µg/g FW) and carotenoid content (135.61 µg/g FW) than the control and other treatments (T2-20 mg/L and T3-40 mg/L). However, the application of a high concentration of ZnO-NPs (20 and 40 mg/L) increased the level of antioxidant enzymes (SOD, APX and GR), total crude and soluble protein, proline and TBARS contents. The accumulations of the compounds quercetin-3-β-D-glucoside, luteolin 7-rutinoside and p-coumaric acid were greater in the leaf compared to the shoot and root. A minor variation was observed in genome size in treated plants as compared to the control group. Overall, this study revealed the stimulatory effect of phytomediated ZnO-NPs, which act as bio-stimulants/nano-fertilizers as revealed by more biomass and the higher production of phytochemical compounds in different parts of the E. macrochaetus.

Assessment of Genetic Diversity among Wild Ruta chalepensis L. from the North of Jordan

Ruta chalepensis, known as Fringed Rue, is a small shrub of the Rutaceae family. To date, there is no record of its natural distribution across Jordan, a country located in the eastern part of the Mediterranean basin, and there are no previous studies on its genetic diversity in the region. Therefore, this study was conducted to assess the genetic diversity of R. chalepensis in the northern parts of Jordan using morphological trait and amplified fragment length polymorphism (AFLP) analyses. For the morphological traits, the analysis of variance indicated that there were significant differences between the identified populations. The Shannon diversity indices showed relatively high values, indicating the existence of a high variability among the identified populations. The principal component analysis explained 82% of the variation between the collected plants, and a clear separation of the collected individuals from the Jarash-A, Jarash-B and Ajloun-B populations from the rest of the populations was observed. The heatmap clustering was in general agreement with the results of the principal component analysis, with the plant height, rachis length and plant width considered as the discriminative traits. The AFLP analysis using eight different primer combinations generated 59 polymorphic bands, with an average polymorphism information content value of 0.32. The phylogenetic analysis identified three main clusters, with the first cluster including 65% of the individuals collected from the Jarash and Ajloun provinces, with a clear separation of the Jarash-B population. The AMOVA revealed that the genetic variation between the populations contributed 30% of the total genetic variation, while the variation within the populations explained 70%. In conclusion, morphological traits and molecular markers were used successfully to assess the genetic diversity among wild R. chalepensis from the north of Jordan, and such data can be used for future conservation plans and utilization purposes.

Advancements and future prospective of DNA barcodes in the herbal drug industry

Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.

Aroma Profile and Biological Effects of Ochradenus arabicus Essential Oils: A Comparative Study of Stem, Flowers, and Leaves

The present analysis explores the chemical constituents and determines the in vitro antimicrobial, antidiabetic, and antioxidant significance of the essential oils (EOs) of the stem, leaves, and flowers of Ochradenus arabicus for the first time. The EOs of the flowers presented seventy-four constituents contributing to 81.46% of the total EOs, with the major compounds being 24-norursa-3,12-diene (13.06%), 24-norursa-3,12-dien-11-one (6.61%), and 24-noroleana-3,12-diene (6.25%). The stem EOs with sixty-one compounds contributed 95.95% of the total oil, whose main bioactive compounds were (+)-camphene (21.50%), eremophilene (5.87%), and δ-selinene (5.03%), while a minimum of fifty-one compounds in the leaves’ EOs (98.75%) were found, with the main constituents being n-hexadecanoic acid (12.32%), octacosane (8.62%), tetradecanoic acid (8.54%), and prehydro fersenyl acetone (7.27%). The antimicrobial activity of the EOs of O. arabicus stem, leaves, and flowers was assessed against two bacterial strains (Escherichia coli and Streptococcus aureus) and two fungal strains (Penicillium simplicissimum and Rhizoctonia solani) via the disc diffusion assay. However, the EOs extracted from the stem were found effective against one bacterial strain, E. coli, and one fungal strain, R. Solani, among the examined microbes in comparison to the standard and negative control. The tested EOs samples of the O. arabicus stem displayed a maximum potential to cure diabetes with an IC50 = 0.40 ± 0.10 µg/mL, followed by leaves and flowers with an IC50 = 0.71 ± 0.11 µg/mL and IC50 = 10.57 ± 0.18 µg/mL, respectively, as compared to the standard acarbose (IC50 = 377.26 ± 1.20 µg/mL). In addition, the EOs of O. arabicus flowers had the highest antioxidant activity (IC50 = 106.40 ± 0.19 µg/mL) as compared to the standard ascorbic acid (IC50 = 73.20 ± 0.17 µg/mL) using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. In the ABTS assay, the EOs of the same sample (flower) depicted the utmost potential to scavenge the free radicals with an IC50 = 178.0 ± 0.14 µg/mL as compared with the ascorbic acid, having an IC50 of 87.34 ± 0.10 µg/mL the using 2,2-Azino-Bis-3-Ethylbenzothiazoline-6-Sulfonic acid (ABTS) assay. The EOs of all parts of O. arabicus have useful bioactive components due to which they present antidiabetic and antioxidant significance. Furthermore, additional investigations are considered necessary to expose the responsible components of the examined biological capabilities, which would be effective in the production of innovative drugs.

Impact of Phytomediated Zinc Oxide Nanoparticles on Growth and Oxidative Stress Response of In Vitro Raised Shoots of Ochradenus arabicus

Biogenic nanoparticles have potential roles in the growth and development of plants and animals as they are ecofriendly and free of chemical contaminants. In this study, we assessed the effects of phytomediated zinc oxide nanoparticles (ZnONPs) on shoot growth, biochemical markers, and antioxidant system response in Ochradenus arabicus, which is a medicinal plant. The shoot length and fresh and dry weights were found to be higher in groups with 5 and 10 mg/L ZnONPs than in the control. At high concentrations of ZnONPs (50, 100, and 300 mg/L), biomass was decreased in a concentration-dependent manner. The shoot number was observed to be highest at 50 mg/L among all applied concentrations of ZnONPs. The levels of the stress markers proline and TBARS were found to be higher in shoots treated with 100 and 300 mg/L ZnONPs than in the control as well as NP-treated shoots. The levels of antioxidant enzymes were significantly increased at high concentrations of nanoparticles compared with the control. Thus, synthesized phytomediated ZnONPs from shoots of O. arabicus and their application to the same organ of O. arabicus in vitro were found to be effective as a low concentration of nanoparticles promoted shoot growth, resulting in high biomass accumulation. Thus, using green nanotechnology, such endemic plants could be conserved in vitro and multiple shoots could be produced by reducing the phytohormone concentration for multiple uses, such as the production of potential secondary metabolites.

Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification

Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers' reliability. Our analysis suggests that from the unsupervised method, TaxonDNA's All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.

Amelioration of indole acetic acid-induced cytotoxicity in mice using zinc nanoparticles biosynthesized with Ochradenus arabicus leaf extract

The diversity of natural phytochemicals represents an unlimited source for discovery and development of new drugs. Ochradenus arabicus, (family: Resedaceae) a notable medicinal plant displays a high content of flavonoid glycosides. This study investigates a possible preventative role of zinc nanoparticles biosynthesized by O. arabicus leaf extracts (OAZnO NPs) in limiting genotoxicity and cytotoxicity caused by indole acetic acid (IAA) in laboratory mice. ZnO NPs were synthesized using O. arabicus leaf extracts and characterized with UV–visible spectroscopy, scanning electron microscopy (SEM) and X-Ray diffraction (XRD). The mice were randomly distributed into the following six groups: control, OAZnO NPs treated (10 mg/kg BW), IAA treated (50 mg/kg BW); simultaneous treatment, pre-treatment, and post-treatment. Reactive oxygen species (ROS), DNA damage, chromosome aberration, and apoptosis were analyzed as toxicity endpoints. IAA exposure significantly induced production of ROS, DNA damage, apoptosis, chromosome aberrations, and micronuclei. Pre-, post-, and simultaneous treatment with OAZnO NPs ameliorated the damage caused by IAA exposure. Exposure to OAZnO NPs alone caused no toxicity for any endpoint based on comparison to controls. This study demonstrated that IAA-induced cytotoxic damage in mice could be ameliorated by treatment with OAZnO NPs. These findings require additional verification in mechanistic and in vitro studies.

ITS2: An Ideal DNA Barcode for the Arid Medicinal Plant Rhazya Stricta

INTRODUCTION

In Saudi Arabia, Rhazya stricta is a widely used folkloric plant because of its various therapeutic properties. It is sold in herbal markets as a dried powder; however, the absence of visible phenotypic traits in the powder can mask its authenticity. Potential misidentification of this substance threatens consumer health. DNA barcoding could accurately identify this plant regardless of its physical state, however barcoding presents the challenge of variations in marker loci.

OBJECTIVES

The objective of this work was to assess barcode markers from the chloroplast and nuclear regions to determine their taxonomic accuracy in R. stricta barcoding, and select the best marker for this species that could fulfill the authentication test for its fresh and dried samples.

METHOD

In this study, we assessed seven barcode markers from the chloroplast (psbA-trnH, matK, rbcL, rpoB, and rpoC1) and nuclear regions (ITS1and ITS2). We compared DNA sequences of R. stricta from 50 fresh locally collected samples and 10 dried ground samples from the herbal market with the database sequences of R. stricta, R. orientalis, and eight other related species as controls. We utilized three methods (BLAST, nearest distance, and neighbor-joining tree) in this analysis.

RESULT

With the exception of psbA-trnH, all the chloroplast markers determined high similarity with other taxa. However, nuclear ITS2 best distinguished between R. stricta, R. orientalis, and other related species because of its secondary structures, which allowed for more accurate distinctions. A two-locus marker of ITS1 + ITS2 sequences also showed promising results. A two-dimensional image of our proposed marker was generated to more easily handle DNA barcoding applications.

CONCLUSION

Our study indicates that ITS2 is a cost-effective barcoding marker capable of verifying the authenticity of R. stricta and other medicinal plants in order to protect consumer health.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.

A nucleotide signature for identification of Aglaia stellatopilosa Pannell

Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.

DNA barcoding of medicinal plant material for identification

Because of the increasing demand for herbal remedies and for authentication of the source material, it is vital to provide a single database containing information about authentic plant materials and their potential adulterants. The database should provide DNA barcodes for data retrieval and similarity search. In order to obtain such barcodes, several molecular methods have been applied to develop markers that aid with the authentication and identification of medicinal plant materials. In this review, we discuss the genomic regions and molecular methods selected to provide barcodes, available databases and the potential future of barcoding using next generation sequencing.