DNA extraction techniques for genomic analyses of macroalgae

Abstract

Extracting high-quality DNA in large quantities from Phaeophyceae (brown), Rhodophyta (red), and Chlorophyta (green) macroalgae presents a substantial obstacle for modern molecular studies. Macroalgal tissues are rich in polysaccharides and polyphenols that are known to interfere with downstream molecular techniques. These compounds are released during DNA extraction procedures and often persist despite purification attempts. A wide range of DNA extraction and purification methods have been developed in attempts to overcome these challenges. Here, we review methods of macroalgal DNA extraction, including commercial kits. We discuss each method’s merits and limitations, and examine its potential use in both traditional and high-throughput molecular approaches. Finally, we present our own findings from a range of DNA extraction, purification, and sequencing trials based on the commercially available MoBio PowerPlant® Pro and PowerPlant® Clean kits, carried out on a number of Phaeophyceae species. We found that DNA yield and quality can be improved by lengthy soaking of tissue in extraction buffers, altering the homogenization procedures and modifying solutions used. The DNA extraction protocol presented here can be scaled up for high-throughput analyses and preliminary results suggest suitability for next-generation sequencing.