Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes

Korovesi, Artemis G; Ntertilis, Maria; Kouvelis, Vassili N.

doi:10.1016/j.ympev.2018.04.037

Cited by 52 publications

(49 citation statements)

References 67 publications

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“…The mitochondrial ribosomal protein S3, which contributes to the assembly of the mitochondrial small ribosomal subunit and commonly assumed to be one of ancient genes related to the evolution of mitochondrial genomes in eukaryotes (Korovesi et al, 2018), has been known as the only ribosomal FIGURE 3 | Comparative analysis of mitochondrial gene orders among Trichoderma species. Details of gene components (14 core genes and rns gene) used for the comparative analysis were described in Supplementary Table S5, and plots were generated using Circos.…”

Section: Discussionmentioning

confidence: 99%

Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma

Kwak

2020

Front. Microbiol.

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The improvement of biopesticides for use in the agriculture industry requires an understanding of the biological-and ecological principles underlying their behavior in natural environments. The nuclear genomes of members of the genus Trichoderma, which are representative fungal biocontrol agents, have been actively studied in relation to the unique characteristics of these species as effective producers of CAZymes/secondary metabolites and biopesticides, but their mitochondrial genomes have received much less attention. In this study, the mitochondrial genome of Trichoderma atroviride (Hypocreales, Sordariomycetes), which targets wood-decaying fungal pathogens and has the ability to degrade chemical fungicides, was assembled de novo. A 32,758 bp circular DNA molecule was revealed with specific features, such as a few more protein CDS and trn genes, two homing endonucleases (LAGLIDADG-/GIY-YIG-type), and even a putative overlapping tRNA gene, on a closer phylogenetic relationship with T. gamsii among hypocrealean fungi. Particularly, introns were observed with several footprints likely to be evolutionarily associated with the intron dynamics of the Trichoderma mitochondrial genomes. This study is the first to report the complete de novo mitochondrial genome of T. atroviride, while comparative analyses of Trichoderma mitochondrial genomes were also conducted from the perspective of mitochondrial evolution for the first time.

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Section: Discussionmentioning

confidence: 99%

Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma

Kwak

2020

Front. Microbiol.

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“…We found that most of the core PCGs in Polyporales were subjected to purifying selection. However, rps3 gene was under strong positive selection pressure between some species, which may be to better adapt to their lifestyles or surrounding environment 49 .…”

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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“…This intron is also the common intron shared by fungi in Ophiocordycipitaceae (Zhang et al ., ). These results are also consistent to a recent report on fungal mt‐ rps3 evolution (Korovesi et al ., ), which reveals a widespread presence of rps3 in an rnl intron in Pezizomycotina. The widespread presence of the Rps3‐encoding intron might indicate that it invaded Cordycipitaceae since the divergence of the family from its putative sister family Clavicipitaceae.…”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

Fan

Zhang

2019

Environmental Microbiology

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Summary Isaria cicadae is an entomogenous fungus of great medicinal value. Its nuclear genome has been reported, while its mitogenome remains unknown. Herein, we first described its mitogenome and then inferred intron evolution from both intraspecific and interspecific perspectives. The fungus represented the largest mitogenome (56.6 kb in strain CCAD02) known in Cordycipitaceae due to the presence of 25 introns interrupting nine genes. Comparison of three I. cicadae strains revealed intron presence/absence dynamics at six intron loci plus a few indels and single nucleotide polymorphisms. Phylogenetic analyses confirmed the placement of I. cicadae in Cordycipitaceae. Comparison of 10 Cordycipitaceae species revealed a high degree of synteny and conserved genetic content. They, however, varied in intron numbers (1–25 per species) with overall 34 intron loci identified, which resulted in more than twofold variations in mitogenome sizes (24.5–56.6 kb). An rnl intron encoding ribosomal protein S3 was present in all species, suggesting its early invasion in Cordycipitaceae, while further divergence occurred for this intron. The other introns identified in this study were present in some, but not all of the species and have undergone multiple gains and losses in Cordycipitaceae. This study greatly enhanced our understanding of intron evolution in Cordycipitaceae.

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Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes

Cited by 52 publications

References 67 publications

Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma

Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma

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

The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

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