Molecular identification and phylogenetics analysis of southern Indian Amaranthus L. using chloroplast barcodes

Abstract

The genus Amaranthus L. is an underutilized short-lived perennial herb belonging to the Amaranthaceae. Some nutritive-rich species are used as food crops, pseudocereal, and vegetables and are farmed worldwide. Species-level identification of congeners is often complex due to transitional forms and overlapping diagnostic features. Therefore, the current study employed molecular identification and differentiation of five Amaranthus species such as Amaranthus caudatus, A. dubius, A. spinosus, A. tricolor, and A. viridis, using Ribulose 1,5 Biphosphate Carboxylase (rbcL) and Maturase K (matK) chloroplast barcode markers. The DNA extraction and PCR amplification were 100 % successful, and the bidirectional DNA sequencing recovered 607 bp and 820 bp target sequences for rbcL and matK, respectively. Primary validation of DNA sequences of each species using the BLAST algorithm showed the highest similarity between 99.8 % and 100 % with the expected species. The results of nucleotide composition indicated that matK had more variable and parsimony informative sites than the rbcL DNA barcode. The phylogenetic relationship was studied by assembling DNA barcodes for twelve Amaranthus species. The Bayesian likelihood analysis using a concatenated dataset of the rbcL + matK tree revealed two major clades. Clade one comprises seven species, and five other species in two sub-clades formed in the clade two. All the species of Amaranthus resolved as a distinct monophyletic clade, with Celosia argentea as the basal clade. This study provides the foundation for applying DNA barcoding in delineating complex congeners and understanding the genetic relationships. In addition, DNA barcodes obtained from this study could be helpful for stakeholders, consumers, and regulatory agencies to authenticate Amaranthus species traded as functional foods, medicine, and ornamental plants.