Abstract
The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of the Indian 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 Arundinarieae tribes. 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 a taxonomically 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 species may not be informative, and thus, the development of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.
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The sequence data is available in NCBI GenBank
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Acknowledgements
The work was financially supported by Indian Council of Forestry Research and Education (ICFRE), Dehradun as a research project [OG-49/CR-19]. We thank to the Director Forest Research Institute, Dehradun for providing facility for laboratory and field works. We are also very grateful to the Directors of different institute, namely State Forest Research Institute (SFRI) Itanagar, Rain Forest Research Institute (RFRI) Jorhat, Forest Research Centre for Bamboo and Rattan (FRC-BR), Aizawl (Mizoram) for providing access to their bambusetum. The forest departments of Uttarakhand and north eastern states of India are also duly acknowledged for their assistance and permissions in surveys and sample collection from the forest area under their jurisdiction. Finally, we are thankful to Dr. H. B. Naithani (a retired bamboo taxonomist) for his contribution in correct taxonomic identification of the bamboo species.
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The work was financially supported by Indian Council of Forestry Research and Education (ICFRE) as research project [OG-49/CR-19].
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RKM, MSB, and RS involved in project conceptualization, execution, sample collection, and manuscript writing; NN and NU conducted the laboratory work; RKN involved in taxonomic verification of the sample specimen; RKM, AS and SP carried out sequence data analysis; and HSG was the mentor and involved in manuscript writing and editing.
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Meena, R.K., Negi, N., Uniyal, N. et al. Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos. 3 Biotech 10, 534 (2020). https://doi.org/10.1007/s13205-020-02508-7
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DOI: https://doi.org/10.1007/s13205-020-02508-7