A rapid and efficient DNA extraction protocol for Ganoderma zonatum, A basal and upper stem rot pathogen of oil palm in Malaysia

Ganoderma zonatum is associated with both the basal and upper stem rot diseases in oil palm. Despite the severity of these diseases, there is only limited information on the molecular characteristics of this oil palm pathogen. Most of the studies on G. zonatum related to oil palm are focused on the epidemiology and genetic diversity of the organism. In other palm species, G. zonatum has also been identified as the causal agent of bud rot disease. To further characterise the organism using molecular techniques, the ability to isolate good quality DNA samples is important. In this study, seven DNA extraction protocols were evaluated and the best protocol, Boehm protocol, had the highest yield of good quality DNA. The protocol was able to yield 208.95 ± 4.52 µg DNA per gram of sample with purities above 1.80 for A_260/280 and 2.0 for A_260/230. This extraction protocol is a rapid and efficient protocol that employs cetyl trimethylammonium bromide (CTAB), sodium dodecyl sulphate (SDS), β-mercaptoethanol and proteinase K in the lysis buffer. The Boehm protocol was further tested on three other Ganoderma species found in the oil palm plantations and a medicinal fungus, G. lucidum. It was noted that the protocol was efficient, with high yields for G. zonatum when compared to the other four species. This is probably due to the fact that extraction protocols for each organism requires specific optimisation to obtain optimal yield and purity. In conclusion, the Boehm protocol was best suited for genomic DNA extraction of G. zonatum and found suitable for downstream applications such as PacBio sequencing.