Background Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases. Methods The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations. Results Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course during growth in this starvation media identified differential expressed genes (DEGs) that were found to be associated with 30 metabolic pathways. During the active growth phase (Day2), 27 DEGs related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. Several genes associated with mycotoxin biosynthesis were associated with pathogen-host interactions. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course. Conclusions This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.

Ganoderma zonatum (G. 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 characterize 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 optimization 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.

No abstract