Phylogenetic relationships and DNA barcoding of nine endangered medicinal plant species endemic to Saint Katherine protectorate

Abstract

A high degree of endemism has been recorded for several plant groups collectively in Saint Katherine Protectorate (SKP) in the Sinai Peninsula. Nine endangered endemic plant species in SKP were selected to test the variable abilities of three different DNA barcodes; Riboluse-1,5- Biphosphate Carboxylase/Oxygenase Large subunit ( rbcL ), Internal Transcribed Spacer ( ITS ), and the two regions of the plastid gene ( ycf1 ) as well as Start Codon Targeted (SCoT) Polymorphism to find the phylogenetic relationships among them. The three barcodes were generally more capable of finding the genetic relationships among the plant species under study, new barcodes were introduced to the National Centre for Biotechnology Information (NCBI) for the first time through our work. The barcode sequences were efficient in finding the genetic relationships between the nine species. However, SCoT polymorphism could only cluster plant species belonging to the same genus together in one group, but it could not cluster plant species belonging to the same families except for some primers solely. RbcL was the most easily amplified and identified barcode in eight out of the nine species at the species level and the ninth barcode to the genus level. ITS identified all the species to the genus level. Finally, ycf1 identified six out of the eight species, but it could not identify two of the eight species to the genus level.

rbcL gene in global molecular data repository

“…The data in this article gives an overview of the total number of plant species, families, with rbcL gene sequence in the GenBank and the regions that has contributed to the growth of the rbcL sequence in the repository. The sequence data of the rbcL gene are used for renewal of phylogenies among the seed plants [1] . The rbcL gene is preferred among other plant genes for phylogenetic studies due to its slower rate of evolutionary changes and the lowest divergence among the plastid genes in flowering plants [2 , 3] .…”

DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates

“…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][40][41][42][43][44][45][46][47]. For medicinal plant identification, some researchers have used a combination of markers between matK, rbcL, trnH-psbA, and ITS2 sequences.…”