The complete mitochondrial genomes of five important medicinal Ganoderma species: Features, evolution, and phylogeny

Li, Qiang; Xiang, Dabing; Wan, Yan; Wu, Qi; Wu, Xiaoyong; Ma, Chengrui; Song, Yue; Zhao, Gang; Huang, Wenli

doi:10.1016/j.ijbiomac.2019.08.003

Cited by 51 publications

(52 citation statements)

References 85 publications

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“…Pcl K was the most widely distributed Pcl in Basidiomycota, and so was presumed to be derived from the phylum's ancestors. Pcl E was only detected in Ganoderma leucocontextum (Li et al 2019e), but this has also been reported in the distantly related Blastocladiella emersonii (Tambor et al 2008), something suggestive of horizontal gene transfer, but difficult to imagine in view of the different ecologies of the two phyla. Different Basidiomycota species, even from within the same genera, could contain different numbers and Pcls of introns, indicating frequent intron loss or acquisition events during the evolution of Fig.…”

Section: Dynamic Changes Of Introns In Cox1 Gene Of Basidiomycotamentioning

confidence: 91%

“…Pcls P, AD, AI, N, and S were present in more than 30% of the species tested, and considered as the common Pcls in Basidiomycota. Pcls E was detected only in the cox1 gene of Ganoderma leucocontextum (MH252534) (Li et al 2019e). However, it was present in the cox1 gene of the distantly related aquatic species Blastocladiella emersonii (Tambor et al 2008) which belongs to the phylum Blastocladiomycota, a situation not readily explained as horizontal gene transfer between fungi which grow in such different environments seems improbable.…”

Section: Intron Dynamics Of Cox1 Gene In Basidiomycotamentioning

confidence: 99%

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Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes

Ren

Xiang

et al. 2020

IMA Fungus

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In this study, the mitogenomes of two Paxillus species were assembled, annotated and compared. The two mitogenomes of Paxillus involutus and P. rubicundulus comprised circular DNA molecules, with the size of 39,109 bp and 41,061 bp, respectively. Evolutionary analysis revealed that the nad4L gene had undergone strong positive selection in the two Paxillus species. In addition, 10.64 and 36.50% of the repetitive sequences were detected in the mitogenomes of P. involutus and P. rubicundulus, respectively, which might transfer between mitochondrial and nuclear genomes. Large-scale gene rearrangements and frequent intron gain/loss events were detected in 61 basidiomycete species, which revealed large variations in mitochondrial organization and size in Basidiomycota. In addition, the insertion sites of the basidiomycete introns were found to have a base preference. Phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies, indicating that mitochondrial genes were reliable molecular markers for analyzing the phylogenetic relationships of Basidiomycota. This study is the first report on the mitogenomes of Paxillus, which will promote a better understanding of their contrasted ecological strategies, molecular evolution and phylogeny of these important ectomycorrhizal fungi and related basidiomycete species.

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Section: Dynamic Changes Of Introns In Cox1 Gene Of Basidiomycotamentioning

confidence: 91%

Section: Intron Dynamics Of Cox1 Gene In Basidiomycotamentioning

confidence: 99%

Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes

Ren

Xiang

et al. 2020

IMA Fungus

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“…Also, in the mt-genome of R. vinicolor intronic regions contributed to expansion (Li et al, 2019c). On the other hand, representatives of Hygrophorus (Agaricales) and Russula (Russulales) have a conserved and reduced mt-genome within only three group I introns (Li et al, 2019d). The mt-genome of Nectria cinnabarina (Hypocreales), a plant pathogenic fungus that provokes cankers on many tree species and coral spot, presented a highly conserved gene composition and order compared to phylogenetically related fungi though they differed in the quantity as well as tRNAs order (Wang et al, 2016).…”

Section: Conservation Vs Plasticitymentioning

confidence: 99%

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management

et al. 2020

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Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.

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“…Asas_ca01). The complete mitochondrial genome of S. hyphaenes was sequenced and de novo assembled according to previously described methods (Li, Liao et al 2018;Li, Xiang et al 2019;Wang et al 2020). Briefly, we extracted the total genomic DNA of S. hyphaenes using a Fungal DNA Kit D3390-00 (Omega Bio-Tek, Norcross, GA).…”

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confidence: 99%

Characterization of the complete mitochondrial genome of Sterigmatomyces hyphaenes (Agaricostilbales: Agaricostilbaceae) and implications for its phylogeny

Tan

Wang

2020

Mitochondrial DNA Part B

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In this study, the complete mitochondrial genome of Sterigmatomyces hyphaenes was sequenced by the next-generation sequencing. The complete mitochondrial genome of S. hyphaenes contained 17 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, and 23 transfer RNA (tRNA) genes. The total size of the S. hyphaenes mitochondrial genome is 26,198 bp, and the GC content of the mitochondrial genome is 42.08%. Phylogenetic analysis based on the combined mitochondrial gene dataset indicated that the mitochondrial genome of S. hyphaenes exhibited a close relationship with that of Rhodotorula mucilaginosa.

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The complete mitochondrial genomes of five important medicinal Ganoderma species: Features, evolution, and phylogeny

Cited by 51 publications

References 85 publications

Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes

Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management

Characterization of the complete mitochondrial genome of Sterigmatomyces hyphaenes (Agaricostilbales: Agaricostilbaceae) and implications for its phylogeny

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