Selection of DNA barcoding loci and phylogenetic study of a medicinal and endemic plant, Plectranthus asirensis J.R.I. Wood from Saudi Arabia.

Genuine medicinal plant materials are very important for potential crude drug production, which can be used to cure many human diseases. DNA barcoding of medicinal plants is an effective way to identify adulterated or contaminated market materials, but it can be quite challenging to generate barcodes and analyze the data to determine discrimination power. The molecular phylogeny of a plant species infers its relationship to other species. We screened the various loci of the nuclear and chloroplast genome for the barcoding of Plectranthus asirensis, an endemic plant of Saudi Arabia. The chloroplast genome loci such as rps16 and rpoB showed maximum similarity to taxa of the same and other genera via BLAST of the National Center for Biotechnology Information (NCBI) GenBank database; hence, they are less preferable for the development of a DNA barcode. However, nrDNA-ITS and chloroplast loci rbcL and rpoC1 showed less similarity via BLAST of the NCBI GenBank database; therefore, they could be used for DNA barcoding for this species.

Selection of DNA barcoding loci for Nepeta deflersiana Schweinf. ex Hedge from chloroplast and nuclear DNA genomes.

Molecular markers, mainly DNA-based are potential tools for DNA barcoding and phylogenetic study. The plant species belonging to the Nepeta genus have important medicinal value because of the presence of nepetalactones, and they have been used to treat human diseases. We amplified nuclear and chloroplast gene loci to develop a DNA barcode and phylogenetic study of Nepeta deflersiana. Among the studied loci, psbA-trnH and rps16 showed less identity within the genus than the other loci using the Basic Local Alignment Search Tool of the National Center for Biotechnology Information GenBank database. These loci can be used for the development of a DNA barcode to identify and preserve the identity of this species. We also constructed the phylogram of N. deflersiana and other Nepeta species retrieved from the GenBank database (nonredundant DNA-internal transcribed spacer). N. deflersiana was placed in the same clade as N. insaurica with a 99% bootstrap value.

Antibacterial activity of leaf extract of Breonadia salicina (Rubiaceae), an endangered medicinal plant of Saudi Arabia.

Wild plants can contain bioactive compounds with potential activity against disease-causing microorganisms. In the Kingdom of Saudi Arabia, there are many plant species that may have antibacterial, antifungal, or antiviral activities, among other properties. We extracted bioactive compounds with methanol as well as with water from leaves of Breonadia salicina, which is an endangered plant found in the wild in Saudi Arabia. These extracts were tested against the bacteria Bacillus subtilis, Pseudomonas aeruginosa, Shigella sonnei, Escherichia coli, and Staphylococcus aureus. Both extracts showed antibacterial activity against all of the microorganisms, and thus, B. salicina leaf extract has potential as an antimicrobial agent for the preservation of foods, instead of synthetic chemical compounds. We found that the methanolic leaf extract was more effective than the aqueous crude extract against B. subtilis, P. aeruginosa, and S. aureus.

Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA.

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.

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

Some species of the genus Ochradenus are difficult to identify based on morphological markers. Similar limitations are found for biochemical markers. We developed genetic markers based on DNA sequences for Ochradenus arabicus, which is an endemic plant to Saudi Arabia, locally utilized as a medicinal shrub. The internal transcribed spacer sequence of nuclear ribosomal DNA and chloroplast (rpoB and rpoC1) markers were more informative than other chloroplast DNA markers. Based on these markers, we were able to discriminate this species from another species of the same genus (O. baccatus) that is widely distributed in Saudi Arabia, despite a high degree of morphological similarity. These genetic markers facilitate its identification, even when acquired in a dried state from local markets.

Assessing molecular signature for some potential date (Phoenix dactylifera L.) cultivars from Saudi Arabia, based on chloroplast DNA sequences rpoB and psbA-trnH.

Phoenix dactylifera L. (date palm), being economically very important, is widely cultivated in the Middle East and North Africa, having about 400 different cultivars. Assessment of date cultivars under trading and farming is a widely accepted problem owing to lack of a unique molecular signature for specific date cultivars. In the present study, eight different cultivars of dates viz., Khodry, Khalas, Ruthana, Sukkari, Sefri, Segae, Ajwa and Hilali were sequenced for rpoB and psbA-trnH genes and analyzed using bioinformatics tools to establish a cultivar-specific molecular signature. The combined aligned data matrix was of 1147 characters, of which invariable and variable sites were found to be 958 and 173, respectively. The analysis clearly reveals three major groups of these cultivars: (i) Khodary, Sefri, Ajwa, Ruthana and Hilali (58% BS); (ii) Sukkari and Khalas (64% BS); and (iii) Segae. The economically most important cultivar Ajwa showed similarity with Khodary and Sefri (67% BS).The sequences of the date cultivars generated in the present study showed bootstrap values between 38% and 70% so these sequences could be carefully used as molecular signature for potential date cultivars under trading and selection of genuine cultivars at the seedling stage for farming.

Molecular authentication of the medicinal herb Ruta graveolens (Rutaceae) and an adulterant using nuclear and chloroplast DNA markers.

Dried parts of different plant species often look alike, especially in powdered form, making them very difficult to identify. Ruta graveolens, sold as a dried medicinal herb, can be adulterated with Euphorbia dracunculoides. The genomic DNA was isolated from the leaf powder (100 mg each) using the modified CTAB method. Internal transcribed spacer sequences of nuclear ribosomal DNA (nrDNA-ITS), and chloroplast spacer sequences (rpoB and rpoC1) are regarded as potential genes for plant DNA barcoding. We amplified and sequenced these spacer sequences and confirmed the sequences with a BLAST search. Sequence alignment was performed using ClustalX to look for differences in the sequences. A DNA marker was developed based on rpoB and rpoC1 of the nrDNA-ITS for the identification of the adulterant E. dracunculoides in samples of R. graveolens that are sold in local herbal markets. Sequence-characterized amplified region markers of 289 and 264 bp for R. graveolens and 424 bp for E. dracunculoides were developed from dissimilar sequences of this nrDNA-ITS to speed up the authentication process. This marker successfully distinguished these species in extracted samples with as little as 5 ng DNA/µL extract.