An An Efficiency of DNA Extraction Methods for Green Microalgae

Main Article Content

Watcharee Kunyalung
Piriya Putanyawiwat
Chaivarakun Chaipanya
Vipa Hongtrakul

Abstract

Microalgae have been known to have numerous medicinal and industrial applications. Molecular studies are important in microalgae research and the study requires suitable concentrations of DNA free of contaminants. At present, numerous protocols exist for DNA extraction from microalgae. However, they are either time-consuming, expensive or work only with few species. In this research, various DNA extraction methods were employed to extract a high concentration of algal DNA with the least contaminants. A total of 30 samples of five algal genus were used in this study. Results indicated that out of five extraction methods, the use of SDS resulted to the highest quality and quantity of DNA, followed by the CTAB method. The extracted algal DNAs obtained from SDS, CTAB, and DTAB methods were suitable for PCR amplification of 18S rDNA region. MseI-digestion was also employed to determine the quality of the isolated algal DNA. The genomic DNA of 24 out of 30, 16 out of 30 and 5 out of 30 algal samples that were extracted using SDS, CTAB, and DTAB methods, respectively, could be digested by MseI. On another hand, the use of Triton x-100 and Chelex -100 methods resulted to a poor DNA quality.

Downloads

Download data is not yet available.

Article Details

How to Cite
Kunyalung, W., Putanyawiwat, P., Chaipanya, C., & Hongtrakul, V. (2021). An An Efficiency of DNA Extraction Methods for Green Microalgae. Rajamangala University of Technology Srivijaya Research Journal, 13(3), 742–753. Retrieved from https://li01.tci-thaijo.org/index.php/rmutsvrj/article/view/244322
Section
Research Article
Author Biographies

Watcharee Kunyalung, Faculty of Science, Kasetsart University

Department of Genetics, Faculty of Science, Kasetsart University, Lat Yao, Chatuchak, Bangkok 10900, Thailand.

Piriya Putanyawiwat, Faculty of Science, Kasetsart University

Department of Genetics, Faculty of Science, Kasetsart University, Lat Yao, Chatuchak, Bangkok 10900,
  Thailand.

Chaivarakun Chaipanya, Faculty of Science, Kasetsart University

Department of Genetics, Faculty of Science, Kasetsart University, Lat Yao, Chatuchak, Bangkok 10900,
  Thailand.

Vipa Hongtrakul, Faculty of Science, Kasetsart University

Department of Genetics, Faculty of Science, Kasetsart University, Lat Yao, Chatuchak, Bangkok 10900,
  Thailand.

References

Aljanabi, S.M. and Martinez, I. 1997. Universal and rapid salt-extraction of high-quality genomic DNA for PCR-based techniques. Nucleic Acids Research 25: 4692-4693.

Barsanti, L., Vismara, R., Passarelli, V. and Gualtieri, P. 2001. Paramylon (β-1,3-glucan) content in wild type and WZSL mutant of Euglena gracilis. Effects of growth conditions. Journal of Applied Phycology 13: 59-65.

Beom-Ho, J., Chang, S.L., Hae-Ryong, S., Hyung-Gwan, L. and Hee-Mock, O. 2014. Development of Novel Microsatellite Markers for Strain-Specific Identification of Chlorella vulgaris. Journal of Microbiology and Biotechnology 24(9): 1189-1195.

Cao, M., Fu, Y., Guo, Y. and Pan, J. 2009. Chlamydomonas (Chlorophyceae) colony PCR. Protoplasma 235: 107-110.

Crysten, E.B.H. and Sabeeha, S.M. 2019. Comparative and Functional Algal Genomics. Annual Review of Plant Biology 70: 605-638.

Doyle, J.J. and Doyle, J.L. 1987. A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical bulletin 19: 11-15.

Doyle, J.J. and Doyle, J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-5.

Friedl, T. 1995. Inferring taxonomic positions and testing genus level assignments in coccoid green lichen algae: a phylogenetic analysis of 18S ribosomal RNA sequences from Dictyochloropsis reticulata and from members of the genus Myrmecia (Chlorophyta, Trebouxiophy- ceae cl. nov.). Journal of Phycology 31: 632-639.

Guillemaut, P. and Drouard, L.M. 1992. Isolation of plant DNA: a fast, inexpensive and reliable method. Plant Molecular Biology Reporter 10: 60-65.

Hill-Ambroz, K.L., Brown-Guedira, G.L. and Fellers, J.P. 2002. Modified rapid DNA extraction protocol for high throughput microsatellite analysis in wheat. Crop Science 42(6): 2088-2091.

John, D.H., Karolina, F., Chien, L., Louise, A.L. and Kenneth, G.K. 2010. An assessment of proposed DNA barcodes in freshwater green algae. Cryptogamie Algologie 31(4): 529-555.

Kwon, H., Su, H.S., Jong, S.L., Sung, R.M., Suk, M.K., Jang, R.L., Dongsu, C. and Won, J.J. 2010. Rapid and simple method for DNA extraction from plant and algal species suitable for PCR amplification using a chelating resin Chelex 100. Plant Biotechnology Report 4: 49-52.

Lodhi, M.A., Ye, G.N., Weeden, N.F. and Reisch, B.I. 1994. A Simple and efficient method for DNA extractions from grapevine cultivars and vitis species. Plant Molecular Biology Reporter 12(1): 6-13.

Lucy, E.E., Russell, D. and Cesar, R.M. 2012. Evaluation of DNA extraction methods for freshwater eukaryotic microalgae. Water Research 46(16): 5355-5364.

Maneeruttanarungroj, C. and Incharoensakdi, A. 2016. Rapid method for DNA isolation from a tough cell wall green alga Tetraspora sp. CU2551. World Journal of Microbiology and Biotechnology 32: 99.

Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from micro-organism. Journal of Molecular Biology 3: 208-218.

Martin, P.C. and Alexander, M. 2018. Trends in microalgae incorporation into innovative food products with potential health benefits. Frontiers in Nutrition 5: 1-10.

Marvin, W.F. and Karen, P.F. 2004. A simple and rapid technique for the isolation of DNA from microalgae. Journal of Phycology 40: 223-225.

Michael, A.B. 2018. Chapter 9 - Microalgae in medicine and human health: A historical perspective, pp 195-210. In Microalgae in Health and Disease Prevention. Academic Press, Australia.

Mokhzanni, M., Nor, J.S., Mohd, S.M., Normawaty, M.N. and Raha, A.R. 2016. Decontamination of Chlorella sp. culture using antibiotics and antifungal cocktail treatment. ARPN Journal of Engineering and Applied Sciences 11(1): 104-109.

Muhammad, A.A., Iqrar, A.K., Hafiza, M.N.C., Ishtiaq, A.R., Ahmad, S.K. and Asif, A.K. 2012. Extraction of DNA suitable for PCR applications from mature leaves of Mangifera indica L. Journal of Biomedicine and Biotechnology 13(4): 239-243.

Newman, S.M., Boynton, J.E., Gillham, N.W., Randolph-Anderson, B.L, Johnson, A.M. and Harris, E.H. 1990.

Transformation of chloroplast ribosomal, RNA genes in Chlamydomonas: molecular and genetic characterization of integration events. Genetics 126: 875-888.

Philip, T.P., Lieve, L. and Andy, A. 2011. Making Biofuel from Microalgae. Amarican Scientist 93: 474.

Phillips, N., Smith, C.M. and Morden, C.W. 2001. An effective DNA extraction protocol for brown algae. Phycological Research 49(2): 97-102.

Pirttila, M.A., Hirsikorpi, M., Kamarainen, T., Jaakola, L. and Hohtola, A. 2001. DNA isolation methods for medicinal and aromatic plants. Plant Molecular Biology Reporter 19(3): 273.

Popper, Z.A., Ralet, M.C. and Domozych, D.S. 2014. Plant and algal cell walls: diversity and diversity and functionality. Annals of Botany 114(6): 1043-1048.

Sangwan, R.S., Yadav, U. and Sangwan, N. S. 2000. Isolation of genomic DNA from defatted oil seed residue of opium poppy (Papaver sominiferum). Plant Molecular Biology Reporter 18: 265-270.

Semagn, K., Bjornstad, A. and Ndjiondjop, M.N. 2006. An overview of molecular marker methods for plants. African Journal of Biotechnology 5(25): 2540-2568.

Sevindik, E., Coskun, F., Murathan, Z.T., Paksoy, M. Y. and Uzun, V. 2016. Comparative analysis of the genomic DNA isolation methods on Inula sp., (Asteraceae). Notulae Scientia Biologicae 8(4): 444-450.

Shivji, M.S., Rogers, S.O. and Stanhope, M.J. 1992. Rapid isolation of high molecular weight DNA from marine macroalgae. Marine Ecology Progress Series 84: 197-203.

Sirakov, I.N. 2016. Nucleic Acid Isolation and Downstream Applications, 1-26. In Larramendy, M.L. and Soloneski, S., eds. Nucleic Acids - From Basic Aspects to Laboratory Tools. InTech DTP, Croatia.

Stanier, R.Y., Kunisawa, R., Mandel, M. and Cohen-Bazire, G. 1971. Purification and properties of unicellular blue-green algae (Order Chroococcales). Bacteriological Reviews 35: 171-205.

Su, X. and Gibor, A. 1988. A method for RNA isolation from marine macro-algae. Anal Biochem 174:650-657.

Takashi, M., Tadashi, K., Masahiro, N. and Norishige, Y. 2012. Effective DNA extraction method for fragment analysis using capillary sequencer of the kelp, Saccharina sp. Journal of Applied Phycology 25(1): 337-347.

Tear, C.J.Y., Lim, C., Wu, J. and Zhao, H. 2013. Accumulated lipids rather than the rigid cell walls impede the extraction of genetic materials for effective colony PCRs in Chlorella vulgaris. Microbial Cell Factories 12(1): 106.

Utkarsha, A., Singh, M.K. and Soumya, I. 2018. Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin. Biological Procedures Online 20: 12. https://doi.org/10.1186/s12575-018-0077-6. Jun.2018.

Walsh, PS., Metzger, DA. and Higuchi, R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10: 506-513.

Wang, T.Y., Wang, L., Zhang, J.H. and Dong, W.H. 2011. A simplified universal genomic DNA extraction protocol suitable for PCR. Genetics and Molecular Research 10(1): 519-525.

Ward, AC. 1992. Rapid analysis of yeast transformants using colony PCR. Biotechniques 13: 350.

Zoe, A.P., Marie, C.R. and David, S.D. 2014. Plant and algal cell walls: diversity and functionality. Annals of Botany 114: 1043-1048.