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Plant Science Today (PST)

Research Articles

Vol. 11 No. 2 (2024)

A modified CTAB method for extracting high-quality genomic DNA from aquatic plants

DOI
https://doi.org/10.14719/pst.2850
Submitted
7 August 2023
Published
17-02-2024 — Updated on 01-04-2024
Versions

Abstract

This study introduces a streamlined approach for extractinghigh-quality DNA fromaquatic plants using CTAB, catering to molecular studies. Seven aquatic plant species(Hygrophilaauriculata, Limnophilarepens, Crinum malabaricum, Lagenandraovata, Ludwigiaperuviana, Eichhorniacrassipes, and Ipomoea aquatica) spanning six orderswere subjected toDNA extraction. The method combinesmechanical lysis and chemical treatments to effectively disrupt cells, coupled with RNase treatment and phenol extraction to mitigate RNA and protein contamination. The optimizedCTAB protocol facilitatesthe extraction of high-quality genomic DNA, suitable for amplifying plant barcode genes such as ITS and rbcL, as well asmarkerslike RAPD and ISSR, thereby enhancing the efficiency and reliability of genomic studies in aquatic plants.

References

  1. Wilkie S, Clark MS, Leroy P, Merlino M, Nègre S, Caissard JC, Sourdille P, Lu YH, Bernard M. Genomic DNA isolation, southern blotting and hybridization. In: Clark MS, editor. Plant Molecular biology—ALaboratoryManual. Springer. Springer, Berlin, Heidelberg. 1997;p. 3-53. https://doi.org/10.1007/978-3-642-87873-2_1
  2. Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research. 1980;8(19):4321-26. https://doi.org/10.1093/nar/8.19.4321
  3. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin. 1987;19:11-15.
  4. Allen G, Flores-Vergara M, Krasynanski S, Kumar S, Thompson W. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature Protocols. 2006;1(5):2320-25.https://doi.org/10.1038/nprot.2006.384
  5. Porebski S, Bailey LG, Baum BR. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter. 1997;15:8-15.https://doi.org/10.1007/BF02772108
  6. Khanuja SP, Shasany AK, Darokar MP, Kumar S. Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Molecular Biology Reporter. 1999;17:1-7.https://doi.org/10.1023/A:1007528101452
  7. Novaes RML, Rodrigues JG, Lovato MB. An efficient protocol for tissue sampling and DNA isolation from the stem bark of Leguminosae trees. Genetics and Molecular Research. 2009;8(1):86-96. https://doi.org/10.4238/vol8-1gmr542
  8. Shioda M, Marakami-Muofushi K. Selective inhibition of DNA polymerase by a polysaccharide purified from slime of Physarumpolycephalum. Biochemical and Biophysical Research Communications. 1987;146(1):61-66. https://10.1016/0006-291x(87)90690-5.
  9. Scott KD, Playford J. DNA extraction technique for PCR in rain forest plant species. Biotechniques. 1996;20(6):974-78. https://doi.org/10.2144/96206bm07
  10. Sharma AD, Gill PK, Singh P. DNA isolation from dry and fresh samples of polysaccharide-rich plants. Plant Molecular Biology Reporter.2002;20:415-415f.https://doi.org/10.1007/BF02772129
  11. Loomis WD. Overcoming problems of phenolics and quinones in the isolation of plant enzymes and organelles. In: Methods in enzymology. Academic Press. 1974; Vol. 31: p. 528-44.https://doi.org/10.1016/0076-6879(74)31057-9
  12. Lodhi MA, Ye GN, Weeden NF, Reisch BI. A simple and efficient method for DNA extraction from grapevine cultivars and Vitisspecies. Plant Molecular Biology Reporter. 1994;12:6-13. https://doi.org/10.1007/BF02668658
  13. Sika KC, Kefela T, Adoukonou-Sagbadja H, Ahoton L, Saidou A, Baba-Moussa L, Baptiste LJ, Kotconi SO, Gachomo EW. A simple and efficient genomic DNA extraction protocol for large scale genetic analyses of plant biological systems. Plant Gene. 2015;1:43-45. https://doi.org/10.1016/j.plgene.2015.03.001
  14. Ahmad SM, Ganaie MM, Qazi PH, Verma V, Basir SF, Qazi GN. Rapid DNA isolation protocol for angiospermic plants. Bulgarian Journal of Plant Physiology. 2004;30:25-33.
  15. Wong LM, Silvaraj S, Phoon LQ. An optimized high-salt CTAB protocol for both DNA and RNA isolation from succulent stems of Hylocereus sp. Journal of Medical and Bioengineering. 2014 Dec;3(4).https://doi.org/10.12720/jomb.3.4.236-240
  16. 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. African Journal of Biotechnology. 2007;6(3):175.
  17. Rogers SO, Bendich AJ. Extraction of DNA from plant tissues. Plant Molecular Biology Manual. 1989;73-83.https://doi.org/10.1007/978-94-009-0951-9_6
  18. Tapia-Tussell R, Quijano-Ramayo A, Rojas-Herrera R, Larque-Saavedra A, Perez-Brito D. A fast, simple and reliable high-yielding method for DNA extraction from different plant species. Molecular Biotechnology. 2005;31(2):137-40. https://doi.org/10.1385/mb:31:2:137
  19. Kang T, Yang M. Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants. BMC Biotechnology. 2004;4(1):20. https://doi.org/10.1186/1472-6750-4-20
  20. Panova M, Aronsson H, Cameron RA, Dahl P, Godhe A, Lind U, Ortega-Martinez O, Pereyra R, Tesson SV, Wrange AL, Blomberg A, Johannesson K.DNA extraction protocols for whole-genome sequencing in marine organisms. Methods of Molecular Biology. 2016;1452:13-44. https://doi.org/10.1007/978-1-4939-3774-5_2
  21. Saeed, Afsharzadeh.,Shabnam, Abbasi. An efficient and simple CTAB based method for total genomic DNA isolation from low amounts of aquatic plants leaves with a high level of secondary metabolites. Progress in Biological Sciences. 2016;6(1):95-106. https://doi.org/10.22059/PBS.2016.59012
  22. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR Protocols: A Guide to Methods and Applications. Academic Press, New York.
  23. ;p.315-22. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
  24. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS one. 2007;2(6):e508.
  25. https://doi.org/10.1371/journal.pone.0000508
  26. Wilson K, Walker J. Principles and techniques of biochemistry and molecular biology. Cambridge University Press. 2005.https://doi.org/10.1017/CBO9780511813412
  27. Moreira PA, Oliveira DA. Leaf age affects the quality of DNA extracted from Dimorphandramollis (Fabaceae), a tropical tree species from the Cerrado region of Brazil. Genetics and Molecular Research. 2011;10(1):353-58. https://doi.org/10.4238/vol10-1gmr1030
  28. SambrookJ,Russell DW. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, New York, USA. 2001.
  29. Paterson AH, Brubaker CL, Wendel JF. A rapid method for extraction of cotton (Gossypiumspp.) genomic DNA suitable for RFLP or PCR analysis. Plant Molecular Biology Reporter. 1993;11:122-27. https://doi.org/10.1007/BF02670470
  30. Maliyakal EJ. An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Research.1992;20:2381. https://doi.org/10.1093/nar/20.9.2381
  31. Fang G, Hammar S, Grumet R. A quick and inexpensive method for removing polysaccharides from plant genomic DNA. Biotechniques. 1992;13(1):52-56.https://doi.org/10.2144/97231bm09

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