Complete Mitochondrial Genome Sequence of the Phytopathogenic Basidiomycete Ganoderma boninense Strain G3

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

doi:10.1128/mra.00968-18

Cited by 5 publications

(6 citation statements)

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“…To date, 13 full Ganoderma mitochondrial genomes have been added to the NCBI database, 9 of which were reported in our prior research ( Li et al, 2019b , 2022d ). We first downloaded the G. applanatum , G. leucocontextum , G. tsugae , G. calidophilum , G. subamboinense , G. meredithae , G. sinense , G. lucidum , G. lucidum s26, G. lucidum s37, G. lingzhi s62, G. lingzhi s74, and G. lingzhi s8 mitochondrial genomes from the NCBI database under the accession numbers KR109212, MH252534, MH252533, MH252535, MW752412, KP410262, KF673550, KC763799, MH252532, MW752414, MW752415, MW752413, and MH252531, respectively ( Li et al, 2013 ; Wang et al, 2016a , b ; Utomo et al, 2019 ; Meng et al, 2022 ). We then obtained the core protein-coding sequence in the mitochondrial genomes of 13 Ganoderma strains.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Xiao

Luo

et al. 2023

Front. Microbiol.

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IntroductionCodon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.MethodsIn this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.ResultsThe codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species.DiscussionThis study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

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Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Xiao

Luo

et al. 2023

Front. Microbiol.

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“…Mitochondrial (mt) DNA has been widely used in evolutionary biology and systematics of Fungi (Paquin et al, 1997;Hausner, 2003;Kouvelis et al, 2004;Formighieri et al, 2008;Pantou et al, 2008;Sethuraman et al, 2009;Duo et al, 2012;Aguileta et al, 2014;Lin et al, 2015;Utomo et al, 2019). As a class of molecular markers, mtDNA sequences have some preferable characteristics in resolving systematic issues, such as faster rate of evolution, the virtual absence of recombination, and conserved gene content (Simon et al, 1994(Simon et al, , 2006Caterino et al, 2000;Lin and Danforth, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…Large variation of mitochondrial genome size in fungi is mainly attributed to different lengths of intronic sequences and intergenic regions (Belcour et al, 1997;Hausner, 2003;Formighieri et al, 2008). Despite with the continuously increasing number of fungal mitochondrial genome studies (Paquin et al, 1997;Hausner, 2003;Formighieri et al, 2008;Pantou et al, 2008;Duo et al, 2012;Torriani et al, 2014;Kang et al, 2017;Zaccaron and Bluhm, 2017;Deng et al, 2018;Utomo et al, 2019), the complete mtDNA sequences available for some important lineages are still limited. There are only 16 complete mitochondrial genomes published from the class Dothideomycetes in GenBank as of December 2019.…”

Section: Introductionmentioning

confidence: 99%

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes

Song

Geng

2020

Front. Microbiol.

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A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core proteincoding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core proteincoding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.

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“…In addition, the complete mitochondrial genome of this fungus is 86,549 bp. The total number of genes encoding for proteins is 51, with 15 conserved proteins, 4 hypothetical proteins, 5 homing endonucleases and 27 tRNAs, as well as small and large rRNA subunits [ 67 ]. Furthermore, a pan-genome analysis of eight draft genomes of Ganoderma sp.…”

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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Complete Mitochondrial Genome Sequence of the Phytopathogenic Basidiomycete Ganoderma boninense Strain G3

Cited by 5 publications

References 5 publications

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes

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

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