Draft Genome Sequence of a Phytopathogenic Ganoderma sp. Strain That Causes Basal Stem Rot Disease on Oil Palm in Sabah, Malaysia

Voo, Christopher Lok Yung; Yeo, Daniel E. T.; Chong, Khim Phin; Rodrigues, Kenneth Francis

doi:10.1128/mra.01240-19

Cited by 4 publications

(2 citation statements)

References 6 publications

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“…With the advancement and improvement of sequencing technologies, genome and transcriptome sequencing has become the approached method in understanding microbial interactions with the environment [ 58 , 59 ], animal hosts [ 60 ] and plant hosts [ 61 , 62 ]. Currently, the genomes of five pathogenic strains of G. boninense have been sequenced: two strains isolated from Indonesia, i.e., the strains NJ3 and G3 [ 63 , 64 ]; and three strains isolated from Malaysia, i.e., PER71, BRIUMSc [ 65 ] and FGV-M [ 66 ]. All genome datasets are freely available from the NCBI database ( Table 1 ).…”

Section: G Boninense Multi-omics Datamentioning

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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Section: G Boninense Multi-omics Datamentioning

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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“…Despite deep interest in fungi, there is little genetic and genomic information available to provide insights into host-interactions [13][14][15] . On the other hand, a complete genome sequence of another Ganoderma fungus, G. lucidum (Gl), revealed remarkable gene cooperation for secondary metabolite biosynthesis as well as the richest sets of wood degradation enzymes among all sequenced basidiomycetes 16 .…”

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confidence: 99%

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

Utomo,

Tanjung,

Aditama

et al. 2024

Sci Rep

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The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

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The Nuclear Genome of Lingzhi Mushroom

Liu

Jiang

et al. 2021

Compendium of Plant Genomes

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Draft Genome Sequence of a Phytopathogenic Ganoderma sp. Strain That Causes Basal Stem Rot Disease on Oil Palm in Sabah, Malaysia

Cited by 4 publications

References 6 publications

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

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

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

The Nuclear Genome of Lingzhi Mushroom

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