Isolation of Genomic DNA From Six Species of Phlogacanthus Nees by Standardized CTAB Method
Abstract
The Phlogacanthus Nees is an ethnomedicinal genus native to North-East India, rich in numerous phytochemical compounds that are pharmacologically significant. Plants from this genus have been used in traditional and herbal medicine. The CTAB extraction method has been employed for the preliminary molecular investigation, specifically for DNA isolation, as the first step towards advanced molecular studies. Total genomic DNA extraction and quantification were carried out in six species of Phlogacanthus Nees, namely Phlogacanthus thyrsiflorus Nees, Phlogacanthus scurviflorus (Wall.) Nees, Phlogacanthus jenkinsii C.B. Clarke, Phlogacanthus quadrangularis (Hook.) Heine, Phlogacanthus guttatus Nees, and Phlogacanthus parviflorus T. Anderson. The CTAB protocol, standardised for this genus, yielded a high quantity of DNA with better concentration and a purity ratio between 1.8 and 2.2, compared to the original standard protocol from fresh leaf tissue. The original protocol produced up to 220 ng/μl, while the kit protocol gave up to 600 ng/μl of DNA concentration. Therefore, the standardised CTAB protocol proved to be the most suitable method for rapid and efficient DNA extraction from the fresh leaf tissue of Phlogacanthus Nees, yielding between 100 and 1500 ng/μl of DNA—substantially higher than the other two protocols. In conclusion, the standardisation of the protocol results in high-quality, concentrated DNA, which is valuable for further molecular biological applications.
Keywords:
Phlogacanthus Nees, ethnomedicinal, CTAB, genomic DNA, quantification
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References
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Huang, J., Ge, X., & Sun, M. (2000). Modified CTAB protocol using a silica matrix for isolation of plant genomic DNA. Biotechniques, 28(3), 432-434. https://doi.org/10.2144/00283bm08
Valiya Thodiyil, J., Edathumthazhe Kuni , S., & Nediyaparambu Sukumaran , P. (2024). A modified CTAB method for extracting high-quality genomic DNA from aquatic plants. Plant Science Today, 11(2), 125–132.https://doi.org/10.14719/pst.2850
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Pooniya, S. K., Tantwai, K., Triphati, N., & Tiwari, S. (2019). A Simple and Efficient Genomic DNA Extraction Protocol for Dried Leaf of Threatened Species Commiphora wightii (Arnott) Bhandari for Genetic Analysis of Plant Biological System. International Journal of Current Microbiology and Applied Sciences, 8(3), 1619-1624. https://doi.org/10.20546/ijcmas.2019.803.188
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Ravindran, A., Gayan, J., & Das, B. N. (2017). A standardized protocol for genomic DNA isolation from the species of Plumbago Linn. International Journal of Life-Sciences Scientific Research, 3(5), 1345-1349. http://dx.doi.org/10.21276/ijlssr.2017.3.5.13
Rosenthal, G. A., & Janzen, D. H. (Eds.). (1979). Herbivores: Their interaction with secondary plant metabolites. Academic Press. https://doi.org/10.1126/science.207.4434.973
Rogstad, S. H. (2003). Plant DNA extraction using silica. Plant Molecular Biology Reporter, 21(4), 463-463. https://doi.org/10.1007/BF02772598
Russo, A., Mayjonade, B., Frei, D., Potente, G., Kellenberger, R. T., Frachon, L., ... & Schlüter, P. M. (2022). Low-input high-molecular-weight DNA extraction for long-read sequencing from plants of diverse families. Frontiers in Plant Science, 13, 883897.https://doi.org/10.3389/fpls.2022.883897
Sahu, S. K., Thangaraj, M., & Kathiresan, K. (2012). DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Molecular Biology, 2012. https://doi.org/10.5402/2012/205049
Schenk, J. J., Becklund, L. E., Carey, S. J., & Fabre, P. P. (2023). What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol. Applications in Plant Sciences, 11(3), e11517.https://doi.org/10.1002/aps3.11517
Scott, K. D., & Playford, J. (1996). DNA extraction technique for PCR in rain forest plant species. Biotechniques, 20(6), 974-978. https://doi.org/10.2144/96206bm07
Sheershika, S., & Ram, M. (2024). Advances in DNA extraction techniques: a comprehensive review of methods and applications. Plant Cell Biotechnology and Molecular Biology, 25(5-6), 30-42. https://doi.org/10.56557/pcbmb/2024/v25i5-68683
Shepherd, M., Cross, M., Stokoe, R. L., Scott, L. J., & Jones, M. E. (2002). High-throughput DNA extraction from forest trees. Plant Molecular Biology Reporter, 20(4), 425-425.https://doi.org/10.1007/BF02772134
Shyu, S. Y., & Hu, J. M. (2013). Comparison of Six DNA Extraction Procedures and the Application of Plastid DNA Enrichment Methods in Selected Non-photosynthetic Plants. Taiwania, 58(4), 268-274.http://dx.doi.org/10.6165/tai.2013.58.268
Singh, S., Bhandari, M. S., & Dwivedi, N. (2025). High-quality DNA extraction for Desmodium gangeticum: A medicinal shrub of Shivalik Himalayas. Journal of Medicinal Plants for Economic Development, 9(1), a272. https://doi.org/10.4102/jomped.v9i1.272
Sinha, S., & Singh, D. (2023). Extraction of high-quality genomic DNA from leaf tissues of marigold. Journal of Ornamental Horticulture, 26(1and2), 79-82. Available at: https://epubs.icar.org.in/index.php/JOH/article/view/151659
Barman, A., Anshumali, B. R., & Marak, C. M. (2017). Rapid seed DNA extraction for species identification and diversity analysis of pumpkin. Journal of Biodiversity and Environmental Sciences, 10(1), 161-168. Available at: https://www.innspub.net/wp-content/uploads/2022/09/JBES-V10-No1-p161-168.pdf
Bailey, D. W., Attia, Z., Reinert, S., S Hulke, B., & Kane, N. C. (2022). Effective strategies for isolating DNA from members of Asteraceae with high concentrations of secondary metabolites. BioTechniques, 72(3), 85-89. https://doi.org/10.2144/btn-2021-0050
Dawodu, O., & Erinle, Q. (2024). Extraction of Genomic DNA from Different Plant Tissues through Phenol-chloroform Method. Annual Research & Review in Biology, 39(11), 51-60. http://dx.doi.org/10.9734/arrb/2024/v39i112155
Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. Available at: https://webpages.charlotte.edu/~jweller2/pages/BINF8350f2011/BINF8350_Readings/Doyle_plantDNAextractCTAB_1987.pdf
Huang, J., Ge, X., & Sun, M. (2000). Modified CTAB protocol using a silica matrix for isolation of plant genomic DNA. Biotechniques, 28(3), 432-434. https://doi.org/10.2144/00283bm08
Valiya Thodiyil, J., Edathumthazhe Kuni , S., & Nediyaparambu Sukumaran , P. (2024). A modified CTAB method for extracting high-quality genomic DNA from aquatic plants. Plant Science Today, 11(2), 125–132.https://doi.org/10.14719/pst.2850
Jobes, D. V., Hurley, D. L., & Thien, L. B. (1995). Plant DNA isolation: a method to efficiently remove polyphenolics, polysaccharides, and RNA. Taxon, 44(3), 379-386. https://doi.org/10.2307/1223408
Khanuja, S. P., Shasany, A. K., Darokar, M. P., & Kumar, S. (1999). Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Molecular Biology Reporter, 17(1), 74.https://doi.org/10.1023/A:1007528101452
Liu, B., Wu, H., Cao, Y., Ma, G., Zheng, X., Zhu, H., ... & Sui, S. (2025). Reducing costs and shortening the cetyltrimethylammonium bromide (CTAB) method to improve DNA extraction efficiency from wintersweet and some other plants. Scientific Reports, 15(1), 13441.https://doi.org/10.1038/s41598-025-94822-4
McDade, L. A., Daniel, T. F., & Kiel, C. A. (2008). Toward a comprehensive understanding of phylogenetic relationships among lineages of Acanthaceae sl (Lamiales). American Journal of Botany, 95(9), 1136-1152. http://dx.doi.org/10.3732/ajb.0800096
Mavrodiev, E. V., Dervinis, C., Whitten, W. M., Gitzendanner, M. A., Kirst, M., Kim, S., ... & Soltis, D. E. (2021). A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa. Applications In Plant Sciences, 9(3), e11413.https://doi.org/10.1002/aps3.11413
Phurailatpam, A. K., Singh, S. R., Chanu, T. M., & Ngangbam, P. (2014). Phlogacanthus - An important medicinal plant of North East India: A review. African Journal of Agricultural Research, 9(26), 2068-2072. http://dx.doi.org/10.5897/AJAR2013.8134
Pooniya, S. K., Tantwai, K., Triphati, N., & Tiwari, S. (2019). A Simple and Efficient Genomic DNA Extraction Protocol for Dried Leaf of Threatened Species Commiphora wightii (Arnott) Bhandari for Genetic Analysis of Plant Biological System. International Journal of Current Microbiology and Applied Sciences, 8(3), 1619-1624. https://doi.org/10.20546/ijcmas.2019.803.188
Prasad, S. H., Ajinath, L. S., & Mathew, D. (2022). Rapid and efficient protocol for genomic DNA extraction from leaf tissues of coconut (Cocos nucifera L.). Horticulture International Journal,6(1)17-21. http://dx.doi.org/10.15406/hij.2022.06.00236
Ravindran, A., Gayan, J., & Das, B. N. (2017). A standardized protocol for genomic DNA isolation from the species of Plumbago Linn. International Journal of Life-Sciences Scientific Research, 3(5), 1345-1349. http://dx.doi.org/10.21276/ijlssr.2017.3.5.13
Rosenthal, G. A., & Janzen, D. H. (Eds.). (1979). Herbivores: Their interaction with secondary plant metabolites. Academic Press. https://doi.org/10.1126/science.207.4434.973
Rogstad, S. H. (2003). Plant DNA extraction using silica. Plant Molecular Biology Reporter, 21(4), 463-463. https://doi.org/10.1007/BF02772598
Russo, A., Mayjonade, B., Frei, D., Potente, G., Kellenberger, R. T., Frachon, L., ... & Schlüter, P. M. (2022). Low-input high-molecular-weight DNA extraction for long-read sequencing from plants of diverse families. Frontiers in Plant Science, 13, 883897.https://doi.org/10.3389/fpls.2022.883897
Sahu, S. K., Thangaraj, M., & Kathiresan, K. (2012). DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Molecular Biology, 2012. https://doi.org/10.5402/2012/205049
Schenk, J. J., Becklund, L. E., Carey, S. J., & Fabre, P. P. (2023). What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol. Applications in Plant Sciences, 11(3), e11517.https://doi.org/10.1002/aps3.11517
Scott, K. D., & Playford, J. (1996). DNA extraction technique for PCR in rain forest plant species. Biotechniques, 20(6), 974-978. https://doi.org/10.2144/96206bm07
Sheershika, S., & Ram, M. (2024). Advances in DNA extraction techniques: a comprehensive review of methods and applications. Plant Cell Biotechnology and Molecular Biology, 25(5-6), 30-42. https://doi.org/10.56557/pcbmb/2024/v25i5-68683
Shepherd, M., Cross, M., Stokoe, R. L., Scott, L. J., & Jones, M. E. (2002). High-throughput DNA extraction from forest trees. Plant Molecular Biology Reporter, 20(4), 425-425.https://doi.org/10.1007/BF02772134
Shyu, S. Y., & Hu, J. M. (2013). Comparison of Six DNA Extraction Procedures and the Application of Plastid DNA Enrichment Methods in Selected Non-photosynthetic Plants. Taiwania, 58(4), 268-274.http://dx.doi.org/10.6165/tai.2013.58.268
Singh, S., Bhandari, M. S., & Dwivedi, N. (2025). High-quality DNA extraction for Desmodium gangeticum: A medicinal shrub of Shivalik Himalayas. Journal of Medicinal Plants for Economic Development, 9(1), a272. https://doi.org/10.4102/jomped.v9i1.272
Sinha, S., & Singh, D. (2023). Extraction of high-quality genomic DNA from leaf tissues of marigold. Journal of Ornamental Horticulture, 26(1and2), 79-82. Available at: https://epubs.icar.org.in/index.php/JOH/article/view/151659
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How to Cite
Boro, N., & Das, B. (2025). Isolation of Genomic DNA From Six Species of Phlogacanthus Nees by Standardized CTAB Method. International Journal of Advancement in Life Sciences Research, 8(3), 128-135. https://doi.org/https://doi.org/10.31632/ijalsr.2025.v08i03.012
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