Abstract
Molecular phylogenetics in general, particularly DNA barcoding, has revolutionized the systematic botany for exact identification of the species with respect to its possible affinities. Pakistan being blessed with a wide range of rare and endemic plants is devoid of critical data on its native flora mostly threatened to the verge of extinction. This paper explores the applicability of DNA barcodes, viz. rbcLa, matK and nrITs for the reconstruction of the phylogeny of Haplophyllum gilesii (Hemsel.) C. C. Townsend, a critically endangered, narrow endemic medicinal plant in Pakistan. The DNA sequences after retrieving from NCBI, for maximum likelihood, near neighbor joining and maximum parsimony, close match and best close match analyses, were performed using MUSCLE, BioEdit, MEGA-7 and TAXONDNA softwares and revealed that the universal plastid barcodes, rbcLa and nrlTs carrying 593 bp and 458 bp, respectively, are effective candidates for precise molecular description of this species, while matK remained as a challenge in this regard. BlastN algorithm successfully matched giving 99% and 96% identity with the reference datasets. The results further confirmed 75% best and best close match for rbcLa 12% while 0.0% for nrITs. Our findings are the first of its nature for Pakistan, which provides a sound foundation for molecular biosystematics of the threatened flora of the region.