The First Mitochondrial Genome for Geastrales (Sphaerobolus stellatus) Reveals Intron Dynamics and Large-Scale Gene Rearrangements of Basidiomycota

Abstract

In this study, the mitogenome of artillery fungus, Sphaerobolus stellatus, was assembled and compared with other Basidiomycota mitogenomes. The Sphaerobolus stellatus mitogenome was composed of circular DNA molecules, with a total size of 152,722 bp. Accumulation of intergenic and intronic sequences contributed to the Sphaerobolus stellatus mitogenome becoming the fourth largest mitogenome among Basidiomycota. We detected large-scale gene rearrangements in Basidiomycota mitogenomes, and the Sphaerobolus stellatus mitogenome contains a unique gene order. The quantity and position classes of intron varied between 75 Basidiomycota species we tested, indicating frequent intron loss/gain events occurred in the evolution of Basidiomycota. A novel intron position classes (P1281) was detected in the Sphaerobolus stellatus mitogenome, without any homologous introns from other Basidiomycota species. A pair of fragments with a total length of 9.12 kb in both the nuclear and mitochondrial genomes of Sphaerobolus stellatus was detected, indicating possible gene transferring events. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies (Bayesian posterior probabilities ≥ 0.99; bootstrap values ≥98). This study served as the first report on the mitogenome from the order Geastrales, which will promote the understanding of the phylogeny, population genetics, and evolution of the artillery fungus, Sphaerobolus stellatus.

The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes

“…The phylum Basidiomycota, the largest group of mushroom-forming fungi on the earth, plays an important role in the natural circulation of forest ecosystems and people's production and life [16] , [17] . The information inferred from mitogenome analyses promoted better understanding of the origin and population genetics of Basidiomycota [18] , [19] . It has been reported that the mitogenomes of Basidiomycota vary greatly in size, genome structure, gene content, gene arrangement, repeat sequence content and intron type [20] , [21] , [22] , [23] .…”

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

“…As evolution progresses, most mitochondrial genes were transferred to the nuclear genome, which was considered to have many advantages (Adams et al, 2002;Adams and Palmer, 2003). However, most fungi retain 14 conserved protein-coding genes for energy metabolism and one rps3 gene, which were called the core PCGs of the fungal mitogenome (Ye et al, 2020). In this study, these core PCGs were found to have high variation rates in the length and base composition even among the closely related species.…”

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

“…The dynamics of introns in Polyporales had a significant effect on Polyporales mitogenome size. The cox1 gene was found to be the largest host gene of introns in Basidiomycota 26 , 27 . In the present study, introns of Polyporales cox1 genes were classified into different position classes (Pcls) using the cox1 gene of Ganoderma calidophilum as a reference 22 , and introns belonging to the same Pcls were considered homologous introns.…”