Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression.

Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg-1 for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg-1 protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.

First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees.

Commiphora gileadensis and C. foliacea (family Burseraceae) are pantropical in nature and known for producing fragrant resin (myrrh). Both the tree species are economically and medicinally important however, least genomic understanding is available for this genus. Herein, we report the complete chloroplast genome sequences of C. gileadensis and C. foliacea and comparative analysis with related species (C. wightii and Boswellia sacra). A modified chloroplast DNA extraction method was adopted, followed with next generation sequencing, detailed bioinformatics and PCR analyses. The results revealed that the cp genome sizes of C. gileadensis and C. foliacea, are 160,268 and 160,249 bp, respectively, with classic quadripartite structures that comprises of inverted repeat's pair. Overall, the organization of these cp genomes, GC contents, gene order, and codon usage were comparable to other cp genomes in angiosperm. Approximately, 198 and 175 perfect simple sequence repeats were detected in C. gileadensis and C. foliacea genomes, respectively. Similarly, 30 and 25 palindromic, 15 and 25 forward, and 20 and 25 tandem repeats were determined in both the cp genomes, respectively. Comparison of these complete cp genomes with C. wightii and B. sacra revealed significant sequence resemblance and comparatively highest deviation in intergenic spacers. The phylo-genomic comparison showed that C. gileadensis and C. foliacea form a single clade with previously reported C. wightii and B. sacra from family Burseraceae. Current study reports for the first time the cp genomics of species from Commiphora, which could be helpful in understanding genetic diversity and phylogeny of this myrrh producing species.

Conservation genetics of endangered medicinal plant Commiphora wightii in Indian Thar Desert.

To ascertain the conservation priorities and strategies for Commiphora wightii, an endangered medicinal plant of Indian Thar Desert, genetic diversity was estimated within and among different populations. The total of 155 amplification products were scored using ten each of RAPD and ISSR primers, exhibiting an overall 86.72% polymorphism across 45 individuals representing eight populations. The cumulative data of two markers were used to compute pair-wise distances. The Neighbor-Joining tree revealed high genetic differentiation among populations except Kiradu population. Nei's gene diversity (h) ranged between 0.082 and 0.193 with total diversity at species level is 0.294. Shannon's information index (I) ranged between 0.118 and 0.275 with an overall diversity of 0.439. Analysis of molecular variance showed more diversity among population level (56.65%) than at within population level (43.35%). The low gene flow value (Nm=0.349) and high coefficient of genetic differentiation (GST=0.589) and high fixation index (FST=0.566) demonstrated elevated genetic differentiation among the population and can be predicted that these populations are not in Hardy-Weinberg proportions. Principal Co-ordinate Analysis confirms that Akal population has become phylogenetically more distinct and less diverse than the rest of the samples. Mantel's test revealed no correlation between genetic and geographical distances of populations (R(2)=0.122). Overall highest diversity was observed in the population of Machiya Safari Park and Kiradu, while lowest in Akal population, later may constitute an evolutionary significant unit, having merit for special management.

Population genetic structure of the endangered and endemic medicinal plant Commiphora wightii.

Commiphora wightii is a medicinally important endangered species endemic to the Thar Desert of Rajasthan, India and adjoining areas of Pakistan. The populations of this species are declining sharply because of its extensive use as a natural herb. Random amplified polymorphic DNA analysis was conducted to find the genetic variation among 7 populations of C. wightii. Of the 100 random primers screened, 44 primers yielded 220 loci. Statistical analysis indicated low genetic diversity (H (pop) = 0.0958; I = 0.1498; mean polymorphic loci = 14.28%), and high genetic differentiation among the populations (G (ST) = 0.3990; AMOVA Phi (ST) of 0.3390; Bayesian theta ((II)) = 0.3002). The low genetic diversity may be due to geographic isolation and restricted gene flow (N (m) = 0.7533) between the fragmented populations. Unsustainable utilization of the plant has fragmented the population continuum which served the purpose of genetic exchange between populations. Mantel's test was performed which revealed a highly significant positive correlation between genetic and geographic distance (r (2) = 0.614, P = 0.023) among the populations studied. Low variation can also be attributed to poor seed setting and the slow growth pattern of the species, which is also an apomict. In UPGMA dendrogram the Commiphora wightii samples were divided into two major and one minor cluster. These findings can serve as a guide to preserving the genetic resources of this medicinal plant species.