An integrative multi-locus DNA barcode library of selected medicinal plants from the United Arab Emirates

A multi-locus DNA barcode reference library was developed for 55 medicinal plant species from the 56 collected in the United Arab Emirates using rbcL, matK, and ITS2 markers, generating 397 high-quality sequences from 146 specimens. The rbcL marker showed the highest amplification (82.71%) and sequencing success (94.41%), while ITS2 and matK exhibited greater sequence variability with nucleotide diversities of 20.35 and 27.88, respectively. Genetic divergence analyses revealed minimal within-species variation for rbcL (mean 0.03%) and higher divergence within genera and families for matK (mean up to 10.12%) and ITS2 (mean up to 22.20%), confirming their complementary resolution across taxonomic levels. Barcode-gap assessments identified persistent delimitation challenges within Zygophyllum and Suaeda, where intra- and interspecific distances overlapped across all three markers. Species delimitation using Assemble Species by Automatic Partitioning (ASAP) correctly classified up to 94.9% of specimens with rbcL, while ITS2 and matK achieved 82.2-82.6% accuracy. Support Vector Machine (SVM) classification substantially improved resolution, achieving 96.82% accuracy for rbcL and 100% for both matK and ITS2. Logical consensus evaluation across marker combinations without sequence concatenation further demonstrated that SVM-based pairwise combinations resolved up to 100% of evaluable species, with rbcL+matK, matK+ITS2, and rbcL+matK+ITS2 all achieving perfect resolution, outperforming ASAP-based combinations for identical marker sets. The reference library provides validated DNA barcodes that support molecular identification, herbal-product authentication, biodiversity assessment, and conservation planning, and contributes to the Arabian Barcode of Life initiative.

The online version contains supplementary material available at 10.1007/s13205-026-04946-1.