Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes

Li, Qiang; Wang, Qiangfeng; Jin, Xin; Chen, Zuqin; Xiong, Chuan; Li, Ping; Liu, Qiaofeng; Huang, Wenli

doi:10.1016/j.ijbiomac.2018.10.029

Cited by 54 publications

(54 citation statements)

References 81 publications

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“…At the order level, no two orders had the same gene order. In addition, we also observed large-scale gene rearrangements at the family or even generic level (Li et al 2018a;Li et al 2018b;Li et al 2019b;Li et al 2019c). The Basidiomycota mitogenome contains more repetitive sequences than animals, which we consider to be one of the main factors resulting in the high variation seen in the mitochondrial genome; this result is consistent with the findings of previous studies (Aguileta et al 2014).…”

Section: Gene Rearrangement Of Basidiomycete Speciessupporting

confidence: 91%

“…However, compared with their animal counterparts, the mitogenomes of fungi have been less studied (Sandor et al 2018), especially that of basidiomycetes in the basidiomycete class Agaricomycetes (the largest mushroom-forming fungal group). The limited studies that have been carried out on fungal mitogenomes have, however, shown that these vary greatly in genome size, gene content, gene arrangement, intron number, and content of repeat sequences, even between closely related species (Li et al 2018c;Li et al 2019b).…”

Section: Introductionmentioning

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: Gene Rearrangement Of Basidiomycete Speciessupporting

confidence: 91%

Section: Introductionmentioning

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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“…The mitochondrial genome of fungi was thought to have a moderate mutation rate, intermediating to that of plants (highest mutation rate) and animals (lowest mutation rate) 61,62 . It was reported that the mitogenome size, gene arrangement, and repetitive sequences of fungi varied greatly between and within species 39,47,48,63 . The largest known Agaricomycetes mitochondrial genome was Rhizoctonia solani 64 , which was 235.85 kb long and contained 127 PCGs, 2 rRNA genes and 26 tRNA genes.…”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

Wang

Lee

Wang

et al. 2020

Sci Rep

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Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

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“…The Blastocladiella sp. mitochondrial genome was assembled and annotated according to previously described methods (Li, Liao, et al 2018;Li, Wang, et al 2018;Li et al 2019aLi et al , 2019b.…”

Section: Blastocladiella; Mitochondrial Genome; Phylogenetic Analysismentioning

confidence: 99%

Mitochondrial genome characterization and phylogenetic analysis of Blastocladiella sp. (Blastocladiales: Blastocladiaceae)

Wang

Liu

2020

Mitochondrial DNA Part B

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In the present study, the complete mitochondrial genome of an early diverging fungus Blastocladiella sp. was assembled by the next-generation sequencing. The complete mitochondrial genome of Blastocladiella sp. is 33, 800 bp in length and consists of 11,620 (34.38%) adenine, 5,047 (14.93%) cytosine, 6,025 (17.83%) guanosine and 11,108 (32.86%) thymine. The genome contains 19 protein-coding genes, 24 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on the combined mitochondrial gene set showed that Blastocladiella sp. has a close relationship with Allomyces macrogynus and Blastocladiella emersonii.

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Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes

Cited by 54 publications

References 81 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

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

Mitochondrial genome characterization and phylogenetic analysis of Blastocladiella sp. (Blastocladiales: Blastocladiaceae)

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