Authentication of medicinally important plants is e ssential for increasingly demands of herbal remedies worldwide. DNA barcoding technology is currently gaining importance as a reliable tool for plant species identification, although one barcode gene is not enough in the exceptions. Short sequence diversity of standardized specific coding gene regions of <i> rbcLa </i> and <i> matK </i> of plastid genome together with noncoding ribosomal internal transcribed spacer 2 (ITS2) marker is used as barcode to compare and differentiate plant species. The success of obtaining sequences of the 29 analyzed plants distributed in 21 families using three different barcode genes <i> rbcLa </i> , <i> matK </i> and ITS2 were 97%, 79% and 75% respectively. Multiple sequence alignment confirmed the medicinal plants at species level by 89.28%, 86.32% and 60.86% obtained through <i> rbcLa </i> , ITS2 and <i> matK </i> barcodes sequences respectively. The genetic distance between sequence pairs (GD) and percentage identity (PI) is compared to analyze the plant identity at species level. The phylogenic trees constructed to show the relatedness and distance of the analyzed plants in the history of evolution by the analysis of richness of clades. The construction of DNA barcode library of desert medicinal plants is an introductory research arena in Kingdom of Bahrain in helping the routine identification of plants, and developing guidelines for detection of adulterants in herbal medicines as well as protection of biodiversity.
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