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Basal stem rot of oil palms (OPs) is caused by Ganoderma boninense, a white-rot fungus. Root tissues are the primary route for G. boninense penetration and subsequent pathogenesis on OPs. Little is known on the host lignin biochemistry and selectivity for G. boninense degradation. Oil palm genotypes with different defense responses to G. boninense (highly tolerant, intermediately tolerant, and susceptible) were assessed for root lignin biochemistry (lignin content and composition), plant functional traits (height, fresh weight, girth), chlorophyll content, and root elemental nutrient content. One-year-old seedlings and five-year-old trees were screened for root thioglycolic acid lignin (TGA) content, lignin composition, and elemental nutrient depositions, while plant functional traits were evaluated in the one-year-old seedlings only. The TGA lignin in all the oil palm seedlings and trees ranged from 6.37 to 23.72 pM µg−1, whereas the nitrobenzene oxidation products showed a syringyl (S)-to-guaiacyl (G) ratios of 0.18–0.48. Tolerant genotypes showed significantly lower lignin content compared to the intermediately tolerant and susceptible genotypes. Likewise, the S/G ratio was higher in genotypes with lower lignin content. The depositions of root Fe, Si, Ti, S, and Cu were significantly different among the oil palm genotypes with the susceptible genotypes showing greater content than the tolerant genotypes.

Aims: This study was designed to examine the enzyme activity of selected virulent isolates of Ganoderma boninense against oil palm. In a separate in vitro assessment, the effect of macronutrients on the mycelial growth of four selected Ganoderma spp. was also tested. Methodology and results: The study involved a comparison of ligninolytic enzymes; lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) profiling of eight isolates of G. boninense, categorized into three levels of aggressiveness, with two control isolates (G. boninense PER71 and G. tornatum NPG1) using solid-state fermentation (SSF). The Principal Component Analysis (PCA) revealed that the isolates had a significant production of ligninolytic enzymes on day 80. The most aggressive isolate, ET61 had the highest Lac production. As for the macronutrient test, mycelial growth for all the Ganoderma spp. was highly affected by potassium (K). Conclusion, significance and impact of study: The findings of this study elucidated the characteristics of G. boninense in relation to enzyme production for the degradation of oil palm lignin and the identification of essential nutrients involved in the survival and growth of Ganoderma spp. The study provides vital information on the pathogenic characteristics of G. boninense isolates involved in biomass degradation along with the role of nutrient on the growth of Ganoderma spp. that may influence basal stem rot (BSR) management in the field. [ABSTRACT FROM AUTHOR]

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene. [ABSTRACT FROM AUTHOR]

Basal stem rot is one of the major diseases of oil palm ( Elaies guineensis Jacq.) caused by pathogenic Ganoderma species. Trichoderma and mycorrhizae were proposed to be able to reduce the disease severity. However, their roles in improving oil palm defence system by possibly inducing defence-related genes in the host are not well characterized. To better understand that, transcript profiles of eleven putative defence-related cDNAs in the roots of oil palm inoculated with Trichoderma harzianum T32 and mycorrhizae at different time points were studied. Transcripts encoding putative Bowman-Birk protease inhibitor (EgBBI2) and defensin (EgDFS) increased more than 2 fold in mycorrhizae-treated roots at 6 weeks post inoculation (wpi) compared to those in controls. Transcripts encoding putative dehydrin (EgDHN), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), type 2 ribosome inactivating protein (EgT2RIP), and EgDFS increased in the oil palm roots treated with T. harzianum at 6 and/or 12 wpi compared to those in the controls. Some of these genes were also expressed in oil palm roots treated with Ganoderma boninense . This study provides an insight of some defence-related genes induced by Trichoderma and mycorrhizae, and their roles as potential agents to boost the plant defence system. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa developed its biocontrol agent property through the production of antifungal derivatives, with the phenazine among them. In this study, the applications of crude phenazine synthesized by Pseudomonas aeruginosa UPMP3 and hexaconazole were comparatively evaluated for their effectiveness to suppress basal stem rot infection in artificially G. boninense-challenged oil palm seedlings. A glasshouse experiment under the randomized completely block design was set with the following treatments: non-inoculated seedlings, G. boninense inoculated seedlings, G. boninense inoculated seedlings with 1 mg/ml phenazine application, G. boninense inoculated seedlings with 2 mg/ml phenazine application and G. boninense inoculated seedlings with 0.048 mg/ml hexaconazole application. Seedlings were screened for disease parameters and plant vigour traits (plant height, plant fresh weight, root fresh, and dry weight, stem diameter, and total chlorophyll) at 1-to-4 month post-inoculation (mpi). The application of 2 mg/ml phenazine significantly reduced disease severity (DS) at 44% in comparison to fungicide application (DS = 67%). Plant vigour improved from 1 to 4 mpi and the rate of disease reduction in seedlings with phenazine application (2 mg/ml) was twofold greater than hexaconazole. At 4, 6 and 8 wpi, an up-regulation of chitinase and β-1,3 glucanase genes in seedlings treated with phenazine suggests the involvement of induced resistance in G. boninense-oil palm pathosystem. [ABSTRACT FROM AUTHOR]

Objective: Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads. Description: The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID. [ABSTRACT FROM AUTHOR]

Abstract: Basal stem rot (BSR) is a major disease of oil palm caused by a pathogenic fungus, Ganoderma boninense. However, the interaction between the host plant and its pathogen is not well characterized. To better understand the response of oil palm to G. boninense, transcript profiles of eleven putative defence-related genes from oil palm were measured by quantitative reverse-transcription (qRT)-PCR in the roots of oil palms treated with G. boninense from 3 to 12 weeks post infection (wpi). These transcripts encode putative Bowman–Birk serine protease inhibitors (EgBBI1 and 2), defensin (EgDFS), dehydrin (EgDHN), early methionine-labeled polypeptides (EgEMLP1 and 2), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), metallothionein-like protein (EgMT), pathogenesis-related-1 protein (EgPRP), and type 2 ribosome-inactivating protein (EgT2RIP). The transcript abundance of EgBBI2 increased in G. boninense-treated roots at 3 and 6wpi compared to those of controls; while the transcript abundance of EgBBI1, EgDFS, EgEMLP1, EgMT, and EgT2RIP increased in G. boninense-treated roots at 6 or 12wpi. Meanwhile, the gene expression of EgDHN was up-regulated at all three time points in G. boninense-treated roots. The expression profiles of the eleven transcripts were also studied in leaf samples upon inoculation of G. boninense and Trichoderma harzianum to identify potential biomarkers for early detection of BSR. Two candidate genes (EgEMLP1 and EgMT) that have different profiles in G. boninense-treated leaves compared to those infected by T. harzianum may have the potential to be developed as biomarkers for early detection of G. boninense infection. [Copyright &y& Elsevier]

• First report on a molecular tool for gene manipulation study in G. boninense via RNA-mediated gene silencing. • Three hpRNA vectors corresponding to different regions of G. boninense Lanosterol 14α-demethylase (GbERG11) were prepared and transformed into G. boninense. • The RNAi- ERG11 transformants displayed reduction in growth up to 57.3 %, expression of GbERG11 up to 32.9 % and ergosterol content up to 42.9 % as compared to the wild type. • The RNAi- ERG11 transformants caused less severe disease symptoms on oil palm plantlets at the initial stages of inoculation study. Oil palm plays an essential role in securing the global vegetable oil supply, is prone to the stem rot disease caused by several basidiomycete Ganoderma species, especially Ganoderma boninense. Various mitigation efforts were initiated aiming to tackle the disease, including the study of the fungal pathogen at omics level. However, the functional genomic study protocol is unavailable for G. boninense , which is required for validating the potential pathogenicity genes identified from this fungal species. This is the first report on the development of a molecular tool for gene manipulation study of G. boninense Lanosterol 14α-demethylase (GbERG11) via RNAi-mediated gene silencing. Three Dicer and six Argonaute homologs were identified based on BLASTn analysis on G. boninense genome database. Three hpRNA vectors corresponding to different regions of GbERG11 were prepared and transformed into G. boninense to generate the RNAi- ERG11 transformants. The RNAi- ERG11 transformants were evaluated based on the growth rate, GbERG11 gene expression, biosynthesis of ergosterol and pathogenesis towards oil palm. The RNAi- ERG11 transformants have shown reduced growth, expression of GbERG11 and ergosterol production compared with the wild type. Three representative transformants with the least GbERG11 gene expression were subjected to oil palm in vitro inoculation study. Results showed that the oil palm plantlets inoculated with RNAi- ERG11 transformant (TGL20–2–4) demonstrated significant reduced infection symptoms at the initial stage of the study. On average, the RNAi- ERG11 transformants (TGL20–2–4 and TGL20–3–1) inoculated with oil palm showed a significant reduction of ERG11 gene expression and produced a lower amount of ergosterol as compared to the wild type. The knowledge generated from this study imparts the understanding on the correlation between GbERG11 gene expression and the biosynthesis of ergosterol and fungal pathogenicity. Furthermore, the gene manipulation tool developed in this study can be applied for functional study of other G. boninense genes especially those that are involved in the fungal pathogenicity. Gene silencing of GbERG11 could be extended to inhibit Ganoderma infection in oil palm via host/spray-induced gene silencing. [ABSTRACT FROM AUTHOR]

Cerato-platanin (CP) proteins are small extracellular proteins that play essential roles in the plant-pathogen interactions of some economically important filamentous fungi. At present, there is a lack of information about the roles of CP proteins secreted by Ganoderma boninense , the causal agent of basal stem rot disease in African oil palm, during the early host-pathogen interaction. This work studies the properties and roles of two CP proteins from G. boninense strain PER71. Using bioassay-guided fractionation and nano-LC-MS/MS analysis, we identified peptide matches for G. sinense ZZ0214-1 CP-like and other elicitor proteins in the culture filtrate of G. boninense strain PER71. We found that GbCP2 and GbCP6, two out of nine CP gene models identified in the fungal genome of G. boninense strain PER71, exhibited potential effector properties. We further validated their effector properties by isolating and characterising their coding regions. Interestingly, GbCP6 showed a significant expression level at 11 days post inoculation, indicating its significance in fungal pathogenesis. On the other hand, GbCP2 did not show differential expression at any sampling point, suggesting a different function or role in the pathogenicity of G. boninense. This study identifies GbCP6 as a potential biomarker for early detection of basal stem rot disease in oil palm. [Display omitted] • Ganoderma boninense secretes hypersensitive response-inducing elicitor proteins. • Nine cerato-platanin homologs are present in the G. boninense fungal genome. • GbCP2 and GbCP6 are effector proteins with potential implications in pathogenesis. • GbCP6 emerges as a potential early biomarker for basal stem rot disease. [ABSTRACT FROM AUTHOR]

Ganoderma boninense is a major pathogen for basal stem rot disease that can depolymerize lignocellulosic materials of the oil palm plant by secreting the cell wall-degrading enzymes. The management of this disease is complicated by the asymptomatic phase mediated by the protein-protein interaction (PPI) between the pathogen's effector and plant proteins. There is a lack of network-wide studies on the PPI to elucidate the action of effectors on plant pathways from a systemic perspective as the computational prediction of host-pathogen PPI (HP PPI) is focused on human interaction. Hence, this minireview explores the current computational methods for predicting HP PPI and proposes an approach to predict PPI between G. boninense and oil palm. [Display omitted] • Prediction of host-pathogen protein-protein interaction (PPI) is focused on humans and their pathogens. • Understanding of the early- and late-stage infection stages of G. boninense is limited. • Omics resources for G. boninense and oil palm support the computational prediction of their PPIs. • The structure-based machine learning method is suggested to predict the G. boninense -oil palm PPIs. [ABSTRACT FROM AUTHOR]

Summary Nitric oxide associated 1 (NOA1) protein is implicated in plant disease resistance and nitric oxide (NO) biosynthesis. A full-length cDNA encoding of NOA1 protein from oil palm ( Elaeis guineensis ) was isolated and designated as EgNOA1 . Sequence analysis suggested that EgNOA1 was a circular permutated GTPase with high similarity to the bacterial YqeH protein of the YawG/YlqF family. The gene expression of EgNOA1 and NO production in oil palm root tissues treated with Ganoderma boninense , the causal agent of basal stem rot (BSR) disease were profiled to investigate the involvement of EgNOA1 during fungal infection and association with NO biosynthesis. Real-time PCR (qPCR) analysis revealed that the transcript abundance of EgNOA1 in root tissues was increased by G. boninense treatment. NO burst in Ganoderma -treated root tissue was detected using Griess reagent, in advance of the up-regulation of the EgNOA1 transcript. This indicates that NO production was independent of EgNOA1 . However, the induced expression of EgNOA1 in Ganoderma -treated root tissues implies that it might be involved in plant defense responses against pathogen infection. [ABSTRACT FROM AUTHOR]