Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamb
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ORIGINAL ARTICLE
Chloroplast‑based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos Rajendra K. Meena1 · Nitika Negi1 · Navendra Uniyal1 · Arzoo Shamoon1 · Maneesh S. Bhandari1 · Shailesh Pandey2 · Ranjana K. Negi3 · Rajesh Sharma4 · Harish S. Ginwal1 Received: 7 July 2020 / Accepted: 24 October 2020 © King Abdulaziz City for Science and Technology 2020
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, rps16trnQ 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. Keywords Bamboo · Chloroplast DNA barcode · matK · Phylogenetic analysis · Unique fixed nucleotides
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02508-7) contains supplementary material, which is available to authorized users.
Bamboos (family-Poaceae, subfamily-Bambusoideae) constitute a large group of taxonomically related perennial grasses comprising 1662 species under 121 genera
* Rajendra K. Meena [email protected]
Rajesh Sharma [email protected]
Nitika Negi [email protected]
Harish S. Ginwal [email protected]
Navendra Uniyal [email protected]
1
Arzoo Shamoon [email protected]
Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun 248 195, Uttarakhand, India
2
Maneesh S. Bhandari [email protected]
Division of Forest Protection, Forest Research Institute, Dehradun 248 006, Uttarakhand, India
3
Shailesh Pandey [email protected]
Botany Division, Forest Research Institute, Dehradun 248 006, Uttarakha
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