The first eleven mitochondrial genomes from the ectomycorrhizal fungal genus (Boletus) reveal intron loss and gene rearrangement

Li, Qiang; Wu, Peng; Li, Lijiao; Feng, Huiyu; Tu, Wenying; Bao, Zhijie; Gui, Mingying; Huang, Wenli

doi:10.1016/j.ijbiomac.2021.01.087

Cited by 47 publications

(41 citation statements)

References 78 publications

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“…In order to investigate the phylogenetic relationships of Boletales species and other Basidiomycota species, we constructed a phylogenetic tree of 79 species based on the combined mitochondrial gene datasets (15 core PCGs) ( Li et al, 2021b ). The mitogenome of Annulohypoxylon stygium from the phylum Ascomycota was used as an outgroup ( Deng et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

Yao

Ren

et al. 2021

Front. Microbiol.

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The genus Pisolithus is a group of global ectomycorrhizal fungi. The characterizations of Pisolithus mitochondrial genomes have still been unknown. In the present study, the complete mitogenomes of two Pisolithus species, Pisolithus microcarpus, and Pisolithus tinctorius, were assembled and compared with other Boletales mitogenomes. Both Pisolithus mitogenomes comprised circular DNA molecules with sizes of 43,990 and 44,054 bp, respectively. Comparative mitogenomic analysis showed that the rps3 gene differentiated greatly between Boletales species, and this gene may be subjected to strong pressure of positive selection between some Boletales species. Several plasmid-derived genes and genes with unknown functions were detected in the two Pisolithus mitogenomes, which needs further analysis. The two Pisolithus species show a high degree of collinearity, which may represent the gene arrangement of the ancestors of ectomycorrhizal Boletales species. Frequent intron loss/gain events were detected in Boletales and basidiomycetes, and intron P717 was only detected in P. tinctorius out of the eight Boletales mitogenomes tested. We reconstructed phylogeny of 79 basidiomycetes based on combined mitochondrial gene dataset, and obtained well-supported phylogenetic topologies. This study served as the first report on the mitogenomes of the family Pisolithaceae, which will promote the understanding of the evolution of Pisolithus species.

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Section: Methodsmentioning

confidence: 99%

Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

Yao

Ren

et al. 2021

Front. Microbiol.

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“…A phylogenetic tree of 77 Basidiomycota species was constructed to investigate the status of Trametes species in the phylum Basidiomycota using previously described methods 33,82 based on the combined mitochondrial gene set (15 core PCGs). We used Annulohypoxylon stygium from the phylum Ascomycota as the outgroup 83 .…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

Chen

et al. 2021

Sci Rep

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Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.

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“…Studies on the fungal mitogenomes have shown that fungal mitogenomes exhibited significant variations in gene order, introns, intergenic regions, genome size, and repetitive sequences (Zhang et al, 2016;Zhang Y.J. et al, 2017;Fourie et al, 2018;Wang et al, 2020a;Li et al, 2021). Despite enormous variations in the fungal genome, the 15 protein-coding genes, including atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and rps3, have been detected in most basidiomycete mitochondrial genomes, which were considered 1 https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/ to be core protein-coding genes (PCGs) in the basidiomycete mitochondrial genomes.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

Feng

et al. 2021

Front. Microbiol.

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In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

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The first eleven mitochondrial genomes from the ectomycorrhizal fungal genus (Boletus) reveal intron loss and gene rearrangement

Cited by 47 publications

References 78 publications

Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

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