DNA barcoding for species resolution in Egyptian lamiaceae: regional insights and conservation applications using <i>rbc</i>L, <i>mat</i>K, and <i>trn</i>H-<i>psb</i>A markers

Abstract

The Lamiaceae family includes numerous aromatic and medicinal species, but morphological similarities between taxa often make accurate identification difficult. This study evaluates the performance of three chloroplast DNA barcoding markers, rbcL, matK and trnH-psbA, in resolving species within Thymus, Mentha and Salvia collected from different ecological regions in Egypt. Amplification and sequencing were successful in all genera with rbcL, although resolution was limited to species level (e.g. genetic distance of 0.0154 between Thymus and Mentha). In contrast, matK and trnH-psbA showed better species discrimination but lower amplification efficiency, especially in Salvia (12.5%). Among all markers, trnH-psbA showed the highest interspecific variability with 172 parsimony-informative sites. Principal coordinate analysis and phylogenetic reconstructions using maximum likelihood, maximum parsimony and Bayesian inference models showed that matK and trnH-psbA better resolved interspecific relationships and geographic clustering patterns. A concatenated tree integrating all markers further improves phylogenetic resolution and supports the use of multi-locus barcoding. This study emphasizes that matK and trnH-psbA, when combined with rbcL, improve taxonomic precision within the Lamiaceae, especially in a poorly studied Mediterranean flora such as that of Egypt. Beyond taxonomy, these results have practical implications for the authentication of medicinal species, biodiversity conservation and quality control in the herbal industry. The barcode reference data generated also contributes to regional and global plant identification databases. Our results support the implementation of multi-locus barcoding strategies to resolve complex plant groups and preserve Egypt’s rich botanical heritage.