Comparison of five DNA extraction methods in three medicinal plants: Peganum harmala L., Tamarix ramosissima Ledeb., and Potentilla reptans L.

Document Type : Original article

Authors

1 School of Biology, Damghan University, Damghan, Semnan, Iran

2 Institute of Biological Sciences, Damghan University, Damghan, Semnan, Iran

3 School of mathematics and computer sciences, Damghan University, Damghan, Semnan, Iran

Abstract

Extracting high-yield, high-quality DNA from plant samples is challenging due to the presence of the cell wall, pigments, and some secondary metabolites. The main CTAB method, two of its modified protocols (beta-mercaptoethanol or ammonium acetate were eliminated), the modified Murray and Thompson method, and the Gene All kit were statistically compared based on the quantity and quality of the total DNA (tDNA) extracted from fresh and dried leaves of three medicinal herbs P. harmala, T. ramosissima, and P. reptans. The suitability of the tDNAs for molecular studies was evaluated by polymerase chain reaction (PCR) of the fragments of the internal transcribed spacer (ITS) in nuclear DNA and the trnL-F region in chloroplast DNA. Some significant differences were found between the tDNAs extracted by five extraction methods. With the exception of P. harmala, where the PCR of both the ITS fragments and the trnL-F region worked successfully in all DNA samples, but only the ITS fragments, not the chloroplast trnL-F region, were amplified in the DNA samples of T. ramosissima and P. reptans. The chloroplast trnL-F region was amplified only in DNA samples extracted from fresh and dried leaves of the three studied herbs using the commercial kit. Gene All kit, the main CTAB method, and its modified protocols were the less time-consuming protocols that yielded DNA suitable for downstream PCR vis-a-vis the modified Murray and Thompson method.

Keywords

References

  1. Ribeiro RA, Lovato MB. Comparative analysis of different DNA extraction protocols in fresh and herbarium specimens of the genus Dalbergia. Genet Mol Res 2007;6:173-187.
  2. Varma A, Padh H, Shrivastava N. Plant genomic DNA isolation: an art or a science. Biotechnol J 2007;2:386-392.
  3. Mornkham T, Wangsomnuk PP, Wangsomnuk P, Jogloy S, Pattanothai A, Fu YB. Comparison of five DNA extraction methods for molecular analysis of Jerusalem artichoke (Helianthus tuberosus). Genet Mol Res 2012;11:572-581.
  4. Abdel-Latif A, Osman G. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 2017;13:1.
  5. Scobeyeva VA, Omelchenko DO, Dyakov LM, Konovalov AS, Speranskaya AS, Krinitsina AA. Comparison of some plant DNA extraction methods. Russ J Genet 2018;54:576-586.
  6. Pipan B, Zupančič M, Blatnik E, Dolničar P, Meglič V. Comparison of six genomic DNA extraction methods for molecular downstream applications of apple tree (Malus X domestica). Cogent Food Agric 2018;4:1540094.
  7. Lucas MS, Carvalho CD, Hypolito GB, Côrtes MC. Optimized protocol to isolate high quality genomic DNA from different tissues of a palm species. Hoehnea 2019;46: e942018.
  8. Zhang J, Stewart JM. Economical and rapid method for extracting cotton genomic DNA. J Cotton Sci 2000;4:193-201.
  9. Križman M, Jakše J, Baričevič D, Javornik B, Prošek M. Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta Agr Slov 2006;87:427-433.
  10. Sahu SK, Thangaraj M, Kathiresan K. DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Mol Biol 2012;14:205049.
  11. Herraiz T, González D, Ancín-Azpilicueta C, Arán VJ, Guillén H. β-Carboline alkaloids in Peganum harmala and inhibition of human monoamine oxidase (MAO). Food Chem Toxicol 2010;48:839-845.
  12. Akhani H. Notes on the flora of Iran: 1. Asparagus (Asparagaceae) and Nitraria (Zygophyllaceae). Edinb J Bot 2002;59:295-302.
  13. Fathiazad F, Azarmi Y, Khodaie L. Pharmacological effects of Peganum harmala seeds extract on isolated rat uterus. Iran J Pharm Sci 2006;2:81-86.
  14. Bahmani M, Rafieian-Kopaei M, Parsaei P, Mohsenzadegan A. The anti-leech effect of Peganum harmala L. extract and some anti-parasite drugs on Limnatis nilotica. Afr J Microbiol Res 2012;6:2586-2590.
  15. Asghari GR, Lockwood GB. Stereospecific Biotransformation of (±) Phenylethyl Propionate by Cell Cultures of Peganum harmala L. Iran Biomed J 2002;6:43-46.
  16. Astulla A, Zaima K, Matsuno Y, Hirasawa Y, Ekasari W, Widyawaruyanti A, Zaini NC, Morita H. Alkaloids from the seeds of Peganum harmala showing antiplasmodial and vasorelaxant activities. J Nat Med 2008;62:470-472.
  17. Shonouda M, Osman S, Salama O, Ayoub A. Toxical effect of Peganum harmala L. leaves on the cotton leaf worm, Spodoptera littoralis Boisd and its parasitoids Microplitis rufiventris Kok. Pak J Boil Sci 2008;15:546-552.
  18. Duan Q, Zhu Z, Wang B, Chen M. Recent progress on the salt tolerance mechanisms and application of tamarisk. Int J Mol Sci 2022;23:3325.
  19. Sultanova N, Makhmoor T, Abilov ZA, Parween Z, Omurkamzinova VB, ur-Rahman A, Choudhary MI. Antioxidant and antimicrobial activities of Tamarix ramosissima. J Ethnopharmacol 2001;78:201-205.
  20. Schiman-Czeika H. Tamaricaceae, in: Rechinger, K.H. (ED). Flora Iranica, vol. 4. Akademische Druck- u. Verlagsanstalt, Graz, pp. 1-17.
  21. Ren X, Bao Y, Zhu Y, Liu S, Peng Z, Zhang Y, Zhou G. Isorhamnetin, hispidulin, and cirsimaritin identified in Tamarix ramosissima barks from southern Xinjiang and their antioxidant and antimicrobial activities. Molecules 2019;24:390.
  22. Watkins F, Pendry B, Sanchez-Medina A, Corcoran O. 2012. Antimicrobial assays of three native British plants used in Anglo-Saxon medicine for wound healing formulations in 10th century England. J Ethnopharmacol 2012;144:408-415.
  23. Ksouri R, Falleh H, Megdiche W, Trabelsi N, Mhamdi B, Chaieb K, Bakrouf A, Magné C, Abdelly C. Antioxidant and antimicrobial activities of the edible medicinal halophyte Tamarix gallica L. and related polyphenolic constituents. Food Chem Toxicol 2009;47: 2083-2091.  
  24. Zielinski J. 1982.Rosaceae L., in: Rechinger, K.H. (Ed.) Flora Iranica, 152. Akademische Druck und Verlagsanstalt, Graz, pp.13-31.
  25. Tumbarski Y, Lincheva V, Petkova N, Nikolova R, Vrancheva R, Ivanov I. Antimicrobial activity of extract from aerial parts of potentilla (Potentilla reptans L.). Indust Technol 2017;4:37-43.
  26. Tomczyk M, Latté KP. Potentilla--A review of its phytochemical and pharmacological profile. J Ethnopharmacol 2009;122:184-204.
  27. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 1987;19:11-15.
  28. Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980;8:4321-4326.
  29. Riahi M, Zarre S, Maassoumi AA, Attar F, Osaloo KS. An inexpensive and rapid method for extracting papilionoid genomic DNA from herbarium specimens. Genet Mol Res 2010;9:1334-1342.
  30. King MG, Roalson EH. Exploring evolutionary dynamics of nrDNA in Carex subgenus Vignea (Cyperaceae). Syst Bot 2008;33:514-524.
  31. Taberlet P, Gielly L, Pautou G, Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 1991;17:1105-1109.
  32. Pirie MD, Vargas MP, Botermans M, Bakker FT, Chatrou LW. Ancient paralogy in the cpDNA trnL‐F region in Annonaceae: implications for plant molecular systematics. Am J Bot 2007;94:1003-1016.
  33. Kan XZ, Wang SS, Ding X, Wang XQ. Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications. Mol Phylogenet Evol 2007;44:765-777.
  34. van Wieren-de Wijer DB, Maitland-van der Zee AH, de Boer A, Belitser SV, Kroon AA, de Leeuw PW, Schiffers P, Janssen RG, van Duijn CM, Stricker BH, Klungel OH. Determinants of DNA yield and purity collected with buccal cell samples. Eur J Epidemiol 2009;24:677-682.
  35. Maniatis T, Fritsch EF, Sambrook J. Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1982; 11: 82.
  36. Khare P, Raj V, Chandra S, Agarwal S. Quantitative and qualitative assessment of DNA extracted from saliva for its use in forensic identification. J Forensic Dent Sci 2014;6:81-85.
  37. Korbie DJ, Mattick JS. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc 2008;3:1452-1456.
  38. Sang T, Crawford DJ, Stuessy TF. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proc Natl Acad Sci USA 1995;92: 6813-6817.
  39. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR-Protocols and applications-A Laboratory Manual 1990; PP:315-322.
  40. Nesbitt M. Use of herbarium specimens in ethnobotany, in: Salick, J., Konchar, K., Nesbitt, M. (Eds.), Curating Biocultural Collections. Royal Botanic Gardens, Kew, pp.313–328.
  41. Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc 2006;1:2320-2325.
  42. Khan S, Qureshi MI, Alam T, Abdin MZ. Protocol for isolation of genomic DNA from dry and fresh roots of medicinal plants suitable for RAPD and restriction digestion. Afr J Biotechnol 2007;6:175-178.
  43. Jadhav KP, Ranjani RV, Senthil N. Chemistry of plant genomic DNA extraction protocol. Bioinfolet 2015;12:543-548.
  44. Arruda SR, Pereira DG, Silva-Castro MM, Brito MG, Waldschmidt AM. An optimized protocol for DNA extraction in plants with a high content of secondary metabolites, based on leaves of Mimosa tenuiflora (Willd.) Poir. (Leguminosae). Genet Mol Res 2017;6:16.
  45. Hammad I, Qari SH. Genetic diversity among Zygophyllum (Zygophyllaceae) populations based on RAPD analysis. Genet Mol Res 2010;14:2412-2420.
  46. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 2008;36:e122.
  47. Atherton RA, McComish BJ, Shepherd LD, Berry LA, Albert NW, Lockhart PJ. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform. Plant Methods 2010;6:1-6.
  48. Shi C, Hu N, Huang H, Gao J, Zhao YJ, Gao LZ. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing. PLoS One 2012;7:e31468.
  49. Sharma P, Joshi N, Sharma A. Isolation of genomic DNA from medicinal plants without liquid nitrogen. Indian J Exp Biol 2010;48:610-614.
  50. Saba Hasan, Prakash J, Vashishtha A, Sharma A, Srivastava K, Sagar F, Khan N, Dwivedi K, Jain P, Shukla S, Gupta SP, Mishra S. Optimization of DNA extraction from seeds and leaf tissues of Chrysanthemum (Chrysanthemum indicum) for polymerase chain reaction. Bioinformation 2012;8:225-228.
  51. Ali Q, Salisu IB, Khan SM, Ahmad N, Shahid AA. A modified method for rapid genomic DNA extraction from tuberose. Bio Scientific Review 2019;1:34-39.
  52. Sharifi-Rad J, Quispe C, Herrera-Bravo J, Semwal P, Painuli S, Özçelik B, Ediz Hacıhasanoğlu F, Shaheen Sh, Sen S, Acharya K, Amirian M, Salgado Castillo CM, Dolores López M, Schoebitz M, Martorell M, Goloshvili T, Al-Harrasi A, Al-Rawahi A, Kumar M, Suleria HAR, Cho WC. Peganum spp.: A comprehensive review on bioactivities and health-enhancing effects and their potential for the formulation of functional foods and pharmaceutical drugs. Oxid Med Cell Longev 2021;2021:5900422.
  53. Radovanovic AM, Cupara SM, Popovic SLj, Tomovic MT, Slavkovska VN, Jankovic SM. Cytotoxic effect of Potentilla reptans L. rhizome and aerial part extracts. Acta Pol Pharm 2013;70:851-854.

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