Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm

Utomo, Condro; Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

doi:10.1128/genomea.00122-18

Cited by 28 publications

(14 citation statements)

References 11 publications

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“…The Ganoderma boninense genome [ 13 ] and G. boninense - Elaeis guineensis interaction transcriptome [ 14 ], were obtained from NCBI and analyzed. An average of 156 and 131 million RNAseq reads were generated from three biological replicates for the two growth conditions: (1) in vitro, i.e., G. boninense grown on artificial media, and (2) in planta , i.e., G. boninense interacting with roots of oil palm seedlings, respectively.…”

Section: Resultsmentioning

confidence: 99%

Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

Dhillon¹,

Hamelin²,

Rollins³

2021

BMC Genomics

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Background The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been found associated with live palm hosts. During the host plant colonization process, a massive transcriptional reorganization helps the fungus evade the host immune response and utilize plant cell wall polysaccharides. Results A publicly available transcriptome of G. boninense - oil palm interaction was surveyed to profile transcripts that were differentially expressed in planta. Ten percent of the G. boninense transcript loci had altered expression as it colonized oil palm plants one-month post inoculation. Carbohydrate active enzymes (CAZymes), particularly those with a role in lignin degradation, and auxiliary enzymes that facilitate lignin modification, like cytochrome P450s and haloacid dehalogenases, were up-regulated in planta. Several lineage specific proteins and secreted proteins that lack known functional domains were also up-regulated in planta, but their role in the interaction could not be established. A slowdown in G. boninense respiration during the interaction can be inferred from the down-regulation of proteins involved in electron transport chain and mitochondrial biogenesis. Additionally, pathogenicity related genes and chitin degradation machinery were down-regulated during the interaction indicating G. boninense may be evading detection by the host immune system. Conclusions This analysis offers an overview of the dynamic processes at play in G. boninense - oil palm interaction and provides a framework to investigate biology of Ganoderma fungi across plantations and landscape.

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Section: Resultsmentioning

confidence: 99%

Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

Dhillon¹,

Hamelin²,

Rollins³

2021

BMC Genomics

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“…Overall, the comparative genome analysis employed in this study succeeded in characterizing carbohydrate-active enzymes and identifying CWDE genes that are involved in plant cell wall degradation and pathogenesis of G. boninense . Further genome analysis of G. boninense strains can be carried out with the recent report of draft genome of G. boninense G3 strain isolated from Indonesian region (Utomo et al, 2018). Correlation between the fungal pathogenicity with CWDE production and other factors can be further validated via targeted transcriptome analysis and gene expression profiling of targeted genes (Isaac et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

“…Despite the important roles of CWDEs in the oil palm pathogenesis, information about genomic features and mechanisms underlying the pathogenicity of G. boninense in oil palm is severely lacking. The necessity for establishing a reliable genetic model for understanding Ganoderma -oil palm interactions is highlighted in recent reports of draft genome sequences of different strains of G. boninense which could facilitate the identification of CWDEs as pathogenicity factors essential for successful invasion of oil palm cells (Sulaiman et al, 2018; Utomo et al, 2018). A deeper understanding on the genetic composition of CWDEs as part of carbohydrate-acting enzymes of G. boninense and the biological mechanisms conferring the fungal ability to produce CWDEs are important in our efforts to elucidate the plant-pathogen interactions at the genome and molecular levels.…”

Section: Introductionmentioning

confidence: 99%

Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis

Ramzi

Ruslan

et al. 2019

PeerJ

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BackgroundG. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels.MethodsIn this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3.ResultsG. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis.DiscussionThis study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.

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“…Information on the lignin degrading ability and pathogenicity factors/effectors/genes that causes G. boninense infection during BSR of OPs is poorly documented. The RNA-seq data of G. boninense obtained from two different conditions (axenic and in planta ) along with the publically available G. boninense genome [5], offer lucrative opportunities to understand the molecular events underpinning growth and BSR disease development; effectors for microhyphae, regulatory network of LME production and pathogenesis factor for penetration and colonization.…”

Section: Objectivementioning

confidence: 99%

RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction

2019

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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.

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Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm

Cited by 28 publications

References 11 publications

Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis

RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction

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