The present study explores the taxonomic delineation of Rubus taxa within south Western Ghats of India. Most of the species are aligned in two major subgenera, Idaeobatus and Malachobatus but were lacking systematic botany. The external morphological study developed fine dichotomous key characters for the discrimination of Rubus under study, but it was inadequate for the closely allied species. Therefore, the delineation of the taxa was studied by using the alignment of molecular sequences from three barcode regions (matK, rbcL, and nrITS) and phylogenetic tree of plastid (matK + rbcL), nuclear (nrITS), and combined (plastid + nuclear) genome was constructed for taxa discrimination. Fifteen Rubus collections were comparatively analyzed for the phylogenetic analysis including the inter-specific distance of eleven taxa and the intra-specific distance of four species. It was observed that the nuclear ITS marker had much higher sequence variations compared to the other loci. Phylogenetic relationship within Rubus is well resolved in combined datasets than nuclear and plastid data separately and in this study, the analyzed samples included in both Idaeobatus and Malachobatus formed a polyphyletic clade in all datasets except plastid phylogeny. Wherein the plastid genome, subgenus Malachobatus have shown more conserved sequences than subgenus Idaeobatus. Whereas, subgenus Malachobatus had shown limited species resolution than Idaeobatus in all barcode markers because a group of species belonging to subgenus Malachobatus has shown inadequate genetic variations within species similar to its limited morphological variability. Hence we considered this group a complex species among southern Western Ghats Rubus and it is recommended further clarification.

The present study explores the taxonomic delineation of Rubus taxa within south Western Ghats of India. Most of the species are aligned in two major subgenera, Idaeobatus and Malachobatus but were lacking systematic botany. The external morphological study developed fine dichotomous key characters for the discrimination of Rubus under study, but it was inadequate for the closely allied species. Therefore, the delineation of the taxa was studied by using the alignment of molecular sequences from three barcode regions (matK, rbcL, and nrITS) and phylogenetic tree of plastid (matK + rbcL), nuclear (nrITS), and combined (plastid + nuclear) genome was constructed for taxa discrimination. Fifteen Rubus collections were comparatively analyzed for the phylogenetic analysis including the inter-specific distance of eleven taxa and the intra-specific distance of four species. It was observed that the nuclear ITS marker had much higher sequence variations compared to the other loci. Phylogenetic relationship within Rubus is well resolved in combined datasets than nuclear and plastid data separately and in this study, the analyzed samples included in both Idaeobatus and Malachobatus formed a polyphyletic clade in all datasets except plastid phylogeny. Wherein the plastid genome, subgenus Malachobatus have shown more conserved sequences than subgenus Idaeobatus. Whereas, subgenus Malachobatus had shown limited species resolution than Idaeobatus in all barcode markers because a group of species belonging to subgenus Malachobatus has shown inadequate genetic variations within species similar to its limited morphological variability. Hence we considered this group a complex species among southern Western Ghats Rubus and it is recommended further studies.