In-silico approaches for discrimination of Curcuma species and their closely related family using the novel technique of DNA Barcoding
DOI:
https://doi.org/10.14719/pst.3317Keywords:
Curcuma, Kali Haldi, DNA Barcoding, PCR, Primers, Zingiberaceae, rbcL, trnLAbstract
In this study, we have discriminated and identified the Genus of Curcuma and related species Zingiberaceae using rbcL and trnL DNA barcode primers. Curcuma genus related to the family Zingiberaceae comprises a significant number of medicinal plants renowned for their use in ethnomedicine, playing a pivotal role in the medical, health, and pharmaceutical sectors. Traditionally, morphological methods alone have proven insufficient for accurately identifying species within this family. However, DNA barcoding technology provides a contemporary solution by utilizing plant DNA sequences for species identification, thus enabling effective conservation efforts. We used DNA barcoding techniques and for analysis used the Maximum Parsimony tree in MEGA 11 with the Kimura 2-parameter (KP model) to analyse the genetic relationships between species. Out of the 13 accessions that were studied, 12 accessions belonged to Curcuma caesia and 1 accession belonged to Curcuma aeruginosa. The genetic relationships observed were correlated with the geographical distributions of these species. It was determined that C. aeruginosa is a mutated species of C. caesia. Additionally, 1 specimen of Alpinia galanga, a plant species related to the Zingiberaceae. Barcode primer trnL primer demonstrated a 92% efficiency during the investigation. The rbcL and trnL loci are recommended as potential barcode markers for discriminating between different plant species. This study developed a comprehensive DNA barcoding database that can confidently differentiate between species by combining morphological and molecular data. This database has the potential to identify adulteration in herbal products, combat illegal trade and adulteration of plant species, and assist in germplasm conservation efforts.
Downloads
References
Škorni?ková J. Taxonomic studies in Indian Curcuma L. Dissertation, Charles University, Prague, Czech Republic 2007.
Ratnasingham S, Hebert PDN. bold: The Barcode of Life Data System (http://www. barcodinglife. org). Molecular ecology notes. 2007;7(3). https://doi.org/10.1111/j.1471-8286.2007.01678.x
Angel GR, Menon N, Vimala B. Essential oil composition of eight starchy Curcuma species. Industrial Crops and Products. 2014;60:233-8. https://doi.org/10.1016/j.indcrop.2014.06.028
Sahu VK, Tantawi K, Sapre S. Improved method of DNA extraction from leaf and rhizome samples of black turmeric (Curcuma caesia) for molecular analysis. Journal of Phytopharmacology.2022a; 11(4): 286-88. https://doi.org/10.31254/phyto.2022.11411
Xiang Z, Wang XQ, Cai X, Zeng S. Metabolomics study on quality control and discrimination of three Curcuma species based on gas chromatograph-mass spectrometry. Phytochemical Analysis. 2011;22(5):411-18.https://doi.org/10.1002/pca.1296
Zhang L, Yang Z, Wei J. Contrastive analysis of chemical composition of essential oil from twelve Curcuma species distributed in China. Industrial Crops and Products. 2017;108:17-25. https://doi.org/10.1016/j.indcrop.2017.06.005
Ravindran PN and Babu KN. Ginger: The Genus Zingiber [1st ed.]. CRC Press.2004.
Vanchhawng L, Lalramnghinglova H. Notes on the genus Hedychium J. Koen. (Zingiberaceae) in Mizoram, northeast India. Int J Waste Resour. 2016;6(3):234. https://doi.org/10.4172/2252-5211.1000234
Sahu, V, Tantwai K, Mishra N. Morphological characterization of Curcuma caesia germplasm collected from different regions of Madhya Pradesh. The Pharma Innovation Journal. 2022b;11(7S): 4080-4084.
Chen J, Xia NH, Zhao JT. Chromosome numbers and ploidy levels of Chinese Curcuma species.Hortscience.2013;48(5):525-30. https://doi.org/10.21273/hortsci.48.5.525
Záveská E, Fér T, Šída O, Krak K, Marhold K, Leong-Škorni?ková J. Phylogeny of Curcuma (Zingiberaceae) based on plastid and nuclear sequences: Proposal of the new subgenus Ecomata.Taxon.2012;61(4):747-63. https://doi.org/10.1002/tax.614004
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard R. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences.1984;81(24):8014-8018. https://doi.org/10.1073/pnas.81.24.8014.
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research. 1994;22(22):4673-4680.
https://doi.org/10.1093/nar/22.22.4673
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series.1999;41:95-98.
Hebert PDN, Cywinska A, Ball SL, DeWaard JR. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences.2003;270(1512):313-321. https://doi.org/10.1098/rspb.2002.2218
Chase MW, Salamin N, Wilkinson ML. Plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society.2005; 360(1462):1889-95. https://doi.org/10.1098/rstb.2005.1720
Amandita FY, Rembold K, Vornam B. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecology and Evolution. 2019;9(4):1858-68.https://doi.org/10.1002/ece3.4875
Cahyaningsih R, Compton LJ, Rahayu S. DNA barcoding medicinal plant species from Indonesia.Plants.2022;11(10):1375. https://doi.org/10.3390/plants11101375
Fazekas AJ, Kuzmina ML, Newmaster. DNA barcoding methods for land plants. Methods Molecular Biology. 2012;858:223-52. https://doi.org/10.1007/978-1-61779-591-6_11
Kress WJ, García-Robledo C, Uriarte M.DNA barcodes for ecology, evolution, and conservation. Trends in Ecology and Evolution. 2015;30(1):25-35. https://doi.org/10.1016/j.tree.2014.10.008
Sucher NJ, Hennell JR, Carles MC. DNA fingerprinting, DNA barcoding, and next-generation sequencing technology in plants. Methods in Molecular Biology.2012;862:13-22. https://doi.org/10.1007/978-1-61779-609-8_2
Gravendeel LA, Kouwenhoven MC, Gevaert O. Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Research. 2019;699(23): 9065-9072. https://doi.org/10.1158/0008-5472.CAN-09-2307
Chen S, Yao H, Han J. Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS ONE. 2010;5(1): e8613. https://doi.org/10.1371/journal.pone.0008613
Tsai CC, Chiang YC, Lin YS. Plastid trnL intron polymorphisms among Phalaenopsis species used for identifying the plastid genome type of Phalaenopsis hybrids. Scientia Horticulturae. 2012;142:84-91. https://doi.org/10.1016/j.scienta.2012.05.004
Wongakson P, Rungpragayphan S, Powthongchin B. Evaluation of potential DNA barcodes for identifying Thunbergia spp. Journal of Pharmaceutical Sciences. 2015 10(supple:)147-159.
Osathanunkul MP, Lithanatudom P, Madesis. Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM). Genetics and Molecular Research.2016;15: 13. https://doi.org/10.4238/gmr.15017405
Pettengill JB, Neel MC. An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae).American Journal of Botany. 2010;97(8):1391-406. https://doi.org/10.3732/ajb.0900176
Zurawski G, Gunsalus RP, Brown KD. Structure and regulation of aroH, the structural gene for the tryptophan-repressible 3-deoxy-D-arabino-heptulosonic acid-7-phosphate synthetase of Escherichia coli. Journal of Molecular Biology. 1981;145(1):47-73. https://doi.org/10.1016/0022-2836(81)90334-X
Tripathi AM, Tyagi A, Kumar A. The internal transcribed spacer (ITS) region and trnhH-psbA are suitable candidate loci for DNA barcoding of tropical tree species of India. PloS ONE. 2013;8(2):e57934. https://doi.org/10.1371/journal.pone.0057934
Wang W, Wu Y, Yan Y.DNA barcoding of the Lemnaceae, a family of aquatic monocots. BMC Plant Biology. 2010;10:205. https://doi.org/10.1186/1471-2229-10-205
Chen J, Xia NH. Curcuma gulinqingensis sp.nov. (Zingiberaceae) from Yunnan, China. Nordic Journal of Botany. 2013;31(6):711-6. https://doi.org/10.1111/j.1756-1051.2012.01408.x
Lahaye R, Van der Bank M, Bogarin D. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences. 2008;105(8):2923-8. https://doi.org/10.1073/pnas.0709936105
Downloads
Published
Versions
- 22-07-2024 (2)
- 17-07-2024 (1)
How to Cite
Issue
Section
License
Copyright (c) 2024 Vinod Kumar Sahu , Keerti Tantwai, Sharad Tiwari, Swapnil Sapre, Nishi Mishra , Sobha Sondhia
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright and Licence details of published articles
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
Open Access Policy
Plant Science Today is an open access journal. There is no registration required to read any article. All published articles are distributed under the terms of the Creative Commons Attribution License (CC Attribution 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/by/4.0/). Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
