Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species

Plant Methods

Robert J Henry¹  Tal Cooper¹  Agnelo Furtado¹  Adam Healey¹ 

[1] Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia

关键词: Coffea;    Corymbia;    CTAB;    Next-generation sequencing;    DNA extraction;   

Others  :  1151864
DOI  :  10.1186/1746-4811-10-21

 received in 2014-05-07, accepted in 2014-06-23,  发布年份 2014

【 摘 要 】

Next-generation sequencing technologies rely on high quality DNA that is suitable for library preparation followed by sequencing. Some plant species store large amounts of phenolics and polysaccharides within their leaf tissue making genomic DNA extraction difficult. While many DNA extraction methods exist that contend with the presence of phenolics and polysaccharides, these methods rely on long incubations, multiple precipitations or commercially available kits to produce high molecular weight and contaminant-free DNA. In this protocol, we describe simple modifications to the established CTAB- based extraction method that allows for reliable isolation of high molecular weight genomic DNA from difficult to isolate plant species Corymbia (a eucalypt) and Coffea (coffee). The simplified protocol does not require multiple clean up steps or commercial based kits, and the isolated DNA passed stringent quality control standards for whole genome sequencing on Illumina HiSeq and TruSeq sequencing platforms.

【 授权许可】

   
2014 Healey et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Thermo Scientific: 260/280 and 260/230 Ratios. T009-Technical Bulletin 2008, 1-2.
• [2]Kasem S, Rice N, Henry RJ: DNA Extraction from Plant Tissue. In Plant Genotyping II: SNP Technology Edited by CAB International, Henry RJ. 2008, 219-271.
• [3]Križman M, Jakše J, Baričevič D, Javornik B, Prošek M: Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta Agric Slov 2006, 87:427-433.
• [4]Tibbits JFG, Mcmanus LJ, Spokevicius AV, Bossinger G: A rapid method for tissue collection and high-throughput isolation of genomic DNA from mature trees. Plant Mol Biol Report 2006, 24:81-91.
• [5]Porebski S, Bailey LG, Baum BR: Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Report 1997, 15:8-15.
• [6]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, 2012:1-6.
• [7]Maliyakal JE: An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res 1992, 20:2381.
• [8]Kim CS, Lee CH, Shin JS, Chung YS, Hyung NI: A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucleic Acids Res 1997, 25:1085-1086.
• [9]Khanuja SPS, 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 Mol Biol Report 1999, 17:1-7.
• [10]Labat M, Augur C, Rio B, Perraud-Gaimé I, Sayadi S: Biotechnological Potentialities Of Coffee And Similar With Olive, Two Models Of Agroindustrial Products Rich In Polyphenolic Compounds: A Review. In Coffee Biotechnology and Quality Edited by Kluwer Academic Publishers, Sera T, Soccol CR, Pandey A, Roussos S. 2000, 517-531.
• [11]Asante KS, Brophy JJ, Doran JC, Goldsack RJ, Hibbert DB, Larmour JS: A comparative study of the seedling leaf oils of the spotted gums: species of the Corymbia (Myrtaceae), section Politaria. Aust J Bot 2001, 49:55-66.
• [12]Brophy JJ, Forster PI, Goldsack RJ, Brynn Hibbert D: The essential oils of the yellow bloodwood eucalypts (Corymbia, section Ochraria, Myrtaceae). Biochem Syst Ecol 1998, 26:239-249.
• [13]Doyle J, Doyle J: A rapid procedure for DNA purification from small quantities of fresh leaf tissue. Phytochem Bull 1987, 19:11-15.
• [14]Carrier G, Santoni S, Rodier-Goud M, Canaguier A, De Kochko A, Dubreuil-Tranchant C, This P, Boursiquot J-M, Le Cunff L: An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. Am J Bot 2011, 98:e13-15.
• [15]Peterson DG, Boehm KS, Stack SM: Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), a plant containing high levels of polyphenolic compounds. Plant Mol Biol Report 1997, 15:148-153.
• [16]Shepherd M, Cross M, Stokoe RL, Scott LJ, Jones ME: High-throughput DNA extraction from forest trees. Plant Mol Biol Report 2002, 20:425.
• [17]Furtado A: DNA Extraction from Vegetative Tissue for Next-Generation Sequencing. In Cereal Genomics Methods and Protocols Edited by Springer Protocols, Henry RJ, Furtado A. 2014, 1-5.
• [18]Furtado A, Henry RJ: The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice. Plant Biotechnol J 2005, 3:1-14.
• [19]Couch JA, Fritz PJ: Isolation of DNA from plants high in polyphenolics. Plant Mol Biol Report 1990, 8:8-12.
• [20]Katterman FRH, Shattuck VI: An effective method of DNA isolation from the mature leaves of Gossypium species that contain large amounts of phenolic terpenoids and tannins. Prep Biochem 1983, 13:347-359.
• [21]Henry RJ: Plant DNA Extraction. In Plant Genotyping DNA Fingerprinting Plants Edited by CAB International, Henry RJ. 2001, 239-250.
• [22]Fang G, Hammar S, Grumet R: A quick and inexpensive method for removing polysaccharides from plant genomic DNA. Biotechniques 1992, 13:52-54.
• [23]Ewing B, Green P: Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 1998, 8:186-194.