Comparison of Four DNA Extraction Protocols for Red Seaweeds from Oman: Impacts on Purity, Yield, PCR, and Sequencing Success

DNA barcoding is a reliable technique for seaweed identification. However, high concentrations of sulfated polysaccharides and secondary metabolites hinder the extraction of DNA templates of suitable quality. Therefore, this study assessed four DNA extraction protocols (CTAB, commercial kit, HotSHOT, and DNAzol Direct) using two red seaweed species (Laurencia dendroidea and Hypnea sp.) and two barcoding genes (18S rRNA and rbcL). The results showed significant differences (p < 0.05) in DNA yield (μg/mg), DNA purity (A260/A280), and DNA concentration (ng/μL) among protocols. A significant protocol × seaweed interaction was also observed. DNAzol and HotSHOT provided the highest overall DNA yields (2.390 ± 0.080 and 2.234 ± 0.212 μg/mg, respectively), followed by CTAB (0.123 ± 0.011 μg/mg) and the commercial kit (0.007 ± 0.001 μg/mg). The commercial kit had the highest PCR and DNA sequencing success, followed by HotSHOT, DNAzol, and CTAB. Importantly, DNA concentration and purity did not always correlate with PCR and sequencing success. Considering performance, cost, and processing time, HotSHOT appeared to be the most practical method for Laurencia and Hypnea. This study addresses an important gap in the molecular identification of red seaweeds and provides information for selecting appropriate DNA extraction methods for seaweed barcoding.