Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm (Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

Wong, Wei; Tung, Hun Jiat; Fadhilah, M. Nurul; Midot, Frazer; Lau, Sharon Yu Ling; Melling, Lulie; Astari, S.; Hadziabdic, Ðenita; Trigiano, Robert N.; Goh, K. J.; Goh, Yit Kheng

doi:10.1080/00275514.2021.1884815

Cited by 17 publications

(16 citation statements)

References 46 publications

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“…Notably, there were several core and accessory orthogroups with missing genes, as they were not predicted as genes encoding secreted proteins. G. boninense has a high degree of genetic variability considering its heterothallic mode of reproduction, which requires two compatible partners to produce sexual spores [ 29 , 30 , 31 ]. This has been reflected in the considerably high number of orthogroups in the accessory and in the strain-specific secretome that is typical of the open pan-genome.…”

Section: Resultsmentioning

confidence: 99%

Unveiling the Core Effector Proteins of Oil Palm Pathogen Ganoderma boninense via Pan-Secretome Analysis

Khairi

Muhammad

Bunawan

et al. 2022

JoF

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Ganoderma boninense is the major causal agent of basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, the key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and the annotation of G. boninense T10 were carried out using the Illumina sequencing platform, and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. In total, 320 core orthogroups were enriched with candidate effector proteins (CEPs) that could be classified as carbohydrate-active enzymes, hydrolases, and non-catalytic proteins. Differential expression analysis revealed an upregulation of five CEP genes that was linked to the suppression of PTI signaling cascade, while the downregulation of four CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to transposable elements. The findings obtained from this study aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease.

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Section: Resultsmentioning

confidence: 99%

Unveiling the Core Effector Proteins of Oil Palm Pathogen Ganoderma boninense via Pan-Secretome Analysis

Khairi

Muhammad

Bunawan

et al. 2022

JoF

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“…is completed once the basidiocarp produces basidiospores ( Figure 2 ). The regulation of sexual reproduction by the tetrapolar mating system promotes outbreeding and the diversity of their genetic content in the same plantation area, thus resulting in dynamic populations, and is most probably the primary cause that leads to inefficient disease management [ 16 , 17 ]. The genetic variability was reported to be higher especially for isolates from different geographical origins.…”

Section: G Boninense Life Cyclementioning

confidence: 99%

“…The genetic variability was reported to be higher especially for isolates from different geographical origins. Due to the high divergence of the genetic pool between distinct isolates, different strains exhibit a different degree of aggressiveness and tolerance toward biological control and fungicides [ 6 , 17 , 18 ].…”

Section: G Boninense Life Cyclementioning

confidence: 99%

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Bharudin

Wahab

Samad

et al. 2022

Biology

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Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.

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“…Notably, there were several core and accessory orthogroups with missing genes as they were not predicted as genes encoding secreted proteins. G. boninense has a high degree of genetic variability considering its heterothallic mode of reproduction that requires two compatible partners to produce sexual spores [28][29][30]. This has been reflected in the considerably high number of orthogroups in the accessory and strain-specific secretome that is typical in the open pangenome.…”

Section: The Pan-secretome Of Ganoderma Boninensementioning

confidence: 99%

Unveiling the Core Effector Proteins of Oil Palm Pathogen Ganoderma boninense via Pan-secretome Analysis

Khairi¹,

Muhammad²,

Bunawan³

et al. 2022

Preprint

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Ganoderma boninense is the major causal agent for the basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and annotation of G. boninense T10 were carried out using the Illumina sequencing platform and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised of 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. A set of core candidate effector proteins (CEPs) were found to be enriched with catalytic protein classified as the carbohydrate-active enzymes, hydrolases as well as non-catalytic proteins. Differential expression analysis revealed an upregulation of CEP genes which was linked to the suppression of PTI signaling cascade while the downregulation of CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to the transposable elements. The findings obtained from this study would aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease.

show abstract

Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm (Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

Cited by 17 publications

References 46 publications

Unveiling the Core Effector Proteins of Oil Palm Pathogen Ganoderma boninense via Pan-Secretome Analysis

Unveiling the Core Effector Proteins of Oil Palm Pathogen Ganoderma boninense via Pan-Secretome Analysis

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Unveiling the Core Effector Proteins of Oil Palm Pathogen <i>Ganoderma boninense</i> via Pan-secretome Analysis

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