Emerging methods in botanical DNA/RNA extraction

Abstract

Analyses of nucleic acids (DNA and RNA) have become a staple tool for botanists to answer questions across a wide variety of disciplines, ranging from population genetics to biogeography, ecology, development, microbiology, physiology, and phylogenetics. The rise of “next-generation” or “high-throughput” sequencing in particular has resulted in reduced sequencing costs and an explosion in the number of botanical studies using DNA or RNA data (Egan et al., 2012). Yet, the crucial step of extracting these nucleic acids from plant tissues can be extremely difficult and is often overlooked or under-emphasized. Although there are many options for nucleic acid kits and nearly countless papers (over 22,000 at the time of this special issue) referencing a “modified” version of the Doyle and Doyle (1987) cetyltrimethylammonium bromide (CTAB) extraction protocol, taxon-specific difficulties render many of these methods ineffective. Troubleshooting the extraction step remains a major sink of researchers' time and energy, potentially acting as a barrier to downstream analyses and answering fundamental botanical questions.

Difficulties in nucleic acid extraction arise due to factors such as the diversity and volume of secondary metabolites expressed by plants (Varma et al., 2007), degradation during storage (Pyle and Adams, 1989), contamination from DNA of organisms in the plant microbiome (Trivedi et al., 2022), and the need for high-molecular-weight nucleic acids for downstream analyses (Pollard et al., 2018). Addressing these issues requires knowledge of both the underlying chemistry involved during each step of the extraction process and the requirements of the isolated product. The 12 papers in this special issue, “Emerging Methods in Botanical DNA/RNA Extraction,” highlight the current state of knowledge in nucleic acid extractions, including both the key challenges and creative innovations that have been developed to circumvent these difficulties to address a variety of exciting botanical questions.

N.M. prepared the first draft of the manuscript. All authors provided select article summaries and reviewing and editing assistance and approved the final version of the manuscript.