DNA from Leaf or Stem: A Comparative Work on Dianthus L. for DNA Barcoding Analysis with Four Commercial Extraction Kits

Year 2020, Volume: 48 Issue: 4, 333 - 339, 06.07.2020

Zübeyde Uğurlu Aydın , Mustafa K. Şenova , Marcus Koch , Ali Dönmez

https://doi.org/10.15671/hjbc.663505

Cited By: 1

Abstract

GeneAll GenExTM Plant kiti, GeneMATRIX Plant & Fungi DNA Purification kiti, DNeasy Plant kiti ve E.Z.N.A. Plant DNA kiti yaprak ve gövde dokusu DNA barkodlama çalışmaları için kaliteli ve yüksek genomik DNA elde etmek amacıyla test edilmiştir. Geleneksel olarak yaprak dokusu genomik DNA kaynağı olarak kullanılmaktadır fakat Dianthus taksonları yaprak sklerankima dokusu nedeniyle bu bakımdan sorunludur. Genomik DNA, üretici firmanın sağladığı protokole göre elde edilmiştir ve yedi barkod bölgesi PCR yöntemiyle çoğaltılmıştır. DNA konsantrasyonu florometrik yöntemle ölçülmüş, PCR ürünleri agaroz jelde görüntülenmiştir. Sonuçlar, DNA barkodlama çalışmalarında kullanılabilecek PCR başarısı bakımından değerlendirilmiştir. Ayrıca, kullanılan ekstraksiyon kitleri zahmet, fiyat ve zaman bakımından değerlendirilmiştir.
Sonuçlarımıza göre, yaprak ve gövde dokusundan genomik DNA ekstraksiyonu başarıyla gerçekleştirilmiştir. Tüm ekstraksiyon kitleri PCR amplifikasyonu bakımından başarılı olmasına rağmen en yüksek verim GeneMATRIX kiti kullanılarak elde edilmiştir.

Keywords

Dianthus, DNA barcoding, DNA isolation, PCR success, stem

Thanks

The study was conducted as a part of the project titled “DNA Barcoding Research on some Dianthus L. (Caryophyllaceae) in Turkey” supported by Hacettepe University (FBA-2018-16187).

References

• 1. Z. Xin, J. Chen, A high throughput DNA extraction method with high yield and quality, Plant Methods, 8 (2012) 26.
• 2. M.P. Griffith, M. Porter, Back to the basics: A simple method of DNA extraction for mucilaginous cacti, Bradleya 21 (2003) 26–28.
• 3. J.F. Manen, O. Sinitsyna, L. Aeschbach, A.V. Marlov, A fully automatable enzymatic method for DNA extraction from plant tissues, BMC Plant Biol. Rep. 5 (2005) 23. 4. S. Bashalkhanov, O.P. Rajora, Protocol: A high-throughput DNA extraction system suitable for conifers, Plant Methods 4 (2008) 20.
• 5. J. Steenkamp, I. Wild, A. Lourens, P. Van Helden. Improved method for DNA extraction from Vitis vinifera, Am. J. Enol. Vit. 45 (1994) 102-106.
• 6. S.M. Aljanabi, I. Martinez, Universal and rapid salt-extraction of high quality genomic DNA for PCR based techniques, Nucleic Acids Res. 25 (1997) 4692-4693.
• 7. X. Xu, S. Kawasaki, T. Fujimura, C. Wang, A protocol for highthroughput extraction of DNA from rice leaves, Plant Mol. Biol. Rep. 23 (2005) 291-295.
• 8. E. Sözen, I. Poyraz, Rapid and high quality DNA isolation from Origanum onites for RAPD and ISSR analysis, Z Naturforsch C, 63c (2008) 595-598, 2008.
• 9. D. Yin, H. Liu, X. Zhang, D. Cui, A protocol for extraction of high-quality RNA and DNA from peanut plant tissues, Mol. Biotechnol. 49 (2011) 187-191.
• 10. S.D. Fehlberg, J.M. Allen, K. Church, A novel method of genomic DNA extraction for Cactaceae, Appl. Plant Sci. 1(3) (2013).
• 11. Ç. Karaaslan, H. Akel, S. Ünlü, I. Perçin, Comparison of six commercial DNA extraction kits for DNA extraction from wheat, Hacettepe J. Biol. Chem. 42 (2014) 395-400.
• 12. İ. Poyraz, An efficient DNA isolation method from Nigella sativa L. (Ranunculaceae) seeds for RAPD and ISSR analysis, Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi, 1 (2014) 2148-2330.
• 13. V.A. Scobeyeva, D.O. Omelchenko, L.M. Dyakov, A.S. Konovalov, A.S. Speranskaya, A.A. Krinitsina, Comparison of some plant DNA extraction methods. Russ. J. Genet. 5 (2018) 54.
• 14. J.J. Doyle, J.L. Doyle, A rapid DNA isolation procedure for small quantities of fresh leaf tissue, Phytochemical Bulletin 19 (1987) 11-15.
• 15. D.E. Pearse, K.A. Crandall, F.S.T. Beyond, Analysis of population genetic data for conservation. Conserv. Genet. 5 (2004) 585-602.
• 16. J. Anerao, V. Jha, N. Desai, Optimization of DNA Extraction Methods from Garcinia species for ISSR-PCR, RAPD-PCR and DNA Barcoding, Asian J. Biotechnol. 9 (2017) 35-42.
• 17. M. Akkurt, Comparison between modified DNA extraction protocols and commercial isolation kits in grapevine (Vitis vinifera L.), Genet. Mol. Res. 11(3) (2012) 2343-2351.
• 18. B.D. Lade, A.S. Patil, H.M. Paikrao, Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol, SpringerPlus (2014) 457.
• 19. A. Abdel-Latif, G. Osman, Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize, Plant Methods 13 (2017) 1.
• 20. C.S. Siegel, F.O. Stevenson, E.A. Zimmer, Evaluation and comparison of FTA card and CTAB DNA extraction methods for non‐agricultural taxa, Appl. Plant Sci. 5 (2017) 1600109.
• 21. B. Pipan, M. Zupančič, E. Blatnik, P. Dolničar, V. Meglič, Comparison of six genomic DNA extraction methods for molecular downstream applications of apple tree (Malus X domestica), Cogent Food Agric. 4 (2018) 1540094.
• 22. G. Dittrich‐Schröder, M.J. Wingfield, N.H. Klein, B. Slippers, DNA extraction techniques for DNA barcoding of minute gall‐inhabiting wasps, Mol. Ecol. Resour. 12 (2012) 109−115.
• 23. G. Bacchetta, S. Brullo, M. Casti, G. Giusso del Galdo, Taxonomic revision of the Dianthus sylvestris group (Caryophyllaceae) in central southern Italy, Sicily and Sardinia, Nord. J. Bot. 28 (2010) 137−173.
• 24. L. Dequan, N.J. Turland, Dianthus. In: Wu, Z.Y., Raven, P.H. & Hong, D.Y. (Eds.) Flora of China. Vol. 6. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, 2001, pp. 102-107.
• 25. E. Hamzaoğlu, M. Koç, İ. Büyük, Two new spiny species of Dianthus (Caryophyllaceae) from Turkey, KSU J. Agric. Nat. 21 (2018) 545-554.
• 26. D. Oskay, Dianthus somanus (Caryophyllaceae), a new species from Turkey, Phytotaxa 347 (2018) 263-271.
• 27. İ.G. Deniz, C. Aykurt, İ. Genç, A. Aksoy, A new species of Dianthus (Caryophyllaceae) from Antalya, South Anatolia, Turkey. PhytoKeys 63 (2016) 1-12.
• 28. W. Heise, W. Babik, D. Kubisz, Ł. Kajtoch, DNA barcoding of xerothermic plants, Bot. J. Linn. Soc. 177 (2015) 576-592.
• 29. CBOL Plant Working Group, A DNA barcode for land plants, PNAS USA 106 (2009), 12794-12797.
• 30. R.M.L. Novaes, J.G. Rodrigues, M.B. Lovato, An efficient protocol for tissue sampling and DNA isolation from the stem bark of Leguminosae trees, Genet. Mol. Res. 8 (2009) 86-96.
• 31. Z. Loo, S. Chandran, Extraction of genomic DNA from roots and leaves of Hylocereus undatus, Isr. J. Plant Sci. 60 (2012) 345-348.