Comparative Evaluation of DNA Extraction Protocols for Filamentous Fungi Using Cost-Effective and Broadly Accessible Methods

Abstract

Reliable extraction of high-quality genomic DNA from filamentous fungi remains a technical challenge due to their complex and resilient cell walls. In this study, we conducted a comparative evaluation of five widely used, cost-effective DNA extraction protocols—CTAB, KCl, glass beads, buffer mixture, and microwave—using three filamentous fungal species (Botrytis cinerea, Penicillium spp., and Rhizopus spp.) as test organisms. DNA yield and purity were assessed by spectrophotometric analysis. The buffer mixture protocol emerged as the most consistent and effective, providing both high DNA yields and relatively low levels of contamination. In contrast, the other tested protocols—KCl, CTAB, glass beads, and microwave—showed either high levels of contamination, low reproducibility, or insufficient DNA yield. These findings underscore the importance of selecting extraction methods based on both the biological characteristics of the fungal species and the requirements of downstream applications.