The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales

Abstract

Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85–38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

“…Mitochondria are commonly known as the auxiliary genome of eukaryotes ( Li et al, 2020c , 2023c ). This study found considerable variation in the length and base composition of the mitochondrial core PCGs of various Ganoderma strains, even within the same species, suggesting the differentiation of Ganoderma mitochondrial genes.…”

The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny

“… 2017 ). In the process of long-term evolution, some genes in the mitogenome were lost which was a very common phenomenon observed in mitochondrial genome studies of many fungi (Li et al 2023 ; Li et al 2022 ; Adams et al 2003 ; Adams et al 2002 ). However, a number of genes retained in the mitogenome, including a core set of PCGs, 2 rRNAs with 5-35 tRNAs (Ma et al.…”

“…In addition, further research had found that these introns were mainly classified into groups I and II, with group I introns being relatively abundant in fungal mitogenomes and containing homing endonucleases that might facilitate intron transfer (Li et al. 2023 ). Previous studies found that the cox1 gene was usually the host gene with the highest intron content in the mitogenome (Férandon et al.…”

Lipid Production from Native Oleaginous Yeasts Isolated from Southern Chilean Soil Cultivated in Industrial Vinasse Residues

“…It was decided to reinstate the genus Apiotrichum in order to accommodate species previously assigned to the brassicae/gracile and porosum clades of the genus Trichosporon. The phylogenetic reclassification of Tremellomycetes by Liu et al [68] resulted in the placement of species previously classified in Trichosporon sensu lato into three genera, i.e., Apiotrichum, Cutaneotrichosporon and Trichosporon [69]. It has been reported that some species of Apiotrichum can accumulate lipids.…”