Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos

Abstract

The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of theIndian bamboos. Among 11 chloroplast markers screened, only four, namely matK, rbcL, psbK-I and rps16-trnQ showed successful amplification in 88 genotypes of 30 Indian bamboo taxa under Bambuseae and Arundinarieaetribes. A total of 244 sequences were generated for the four chloroplast regions. Tree-based analysis demonstrated that none of the tested regions successfully discriminated the taxa under Bambuseae tribe. Importantly, our highly concerned Himalayan temperate bamboo species under Arundinarieae tribe, were successfully discriminated by matK locus with high bootstrap support(>60%). Sequence comparisons revealed that the discriminatory power demonstrated by matK region actually lies in the few unique fixed nucleotides (UFNs)despite the overall DNA polymorphism. Although, rps16-trnQ region was found to be the most polymorphic and revealed high genetic divergence among different taxonomic levels, it could not successfully discriminated the taxa with strong statistical support. In ataxonomically difficult plant group like bamboos, whose genome is relatively more complex and has a slow rate of molecular evolution, it is difficult to get a universal marker. Further, highly variable barcode regions utilized in other speciesmay not be informative, and thus, thedevelopment of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.