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.

Keywords: gene rearrangement; intron; mitochondrial genome; phylogenetic analysis; protein coding gene; repeat sequence.

FIGURE 1

Circular map of the mitochondrial genome of Sphaerobolus stellatus. Genes are represented by different colored blocks. Colored blocks outside each ring indicate that the genes are on the direct strand, while colored blocks within the ring indicates that the genes are located on the reverse strand.

FIGURE 2

Putative secondary structures of the 26 tRNA genes identified in the mitochondrial genome of Sphaerobolus stellatus. All genes are shown in order of occurrence in the mitochondrial genome of Sphaerobolus stellatus, starting from trnN.

FIGURE 3

The protein-coding, intronic, intergenic, and RNA gene region proportions of the entire mitochondrial genome of Sphaerobolus stellatus.

FIGURE 4

Codon usage in the mitochondrial genome of Sphaerobolus stellatus. Frequency of codon usage is plotted on the y-axis.

FIGURE 5

Pearson correlation analysis between mitogenome sizes and intron numbers of 75 Basidiomycota species.

FIGURE 6

The insertion sites of different Pcls in cox1 coding regions of 6 basidiomycete species from different orders. The cox1 amino acids of the 6 basidiomycete species were first aligned using Clustal W. The Pcls in red indicate that they are widely distributed introns in the 75 basidiomycetes, while Pcls in blue indicate they are rare Pcls in the 75 basidiomycetes. The symbol ‘Sste’ in green font represents the novel intron identified in Sphaerobolus stellatus. The symbols ‘+1’ and ‘+2’ indicate that the insertion of the intron occurs inside the indicated codon: between the nt 1 and nt 2 of this codon for ‘+1’ and between the nt 2 and nt 3 for ‘+2’. Species ID are shown in Supplementary Table S1.

FIGURE 7

Pcl information of cox1 gene of the 75 Basidiomycota species. The Pcls were name according to its insertion site in the corresponding reference sequence (Ganoderma calidophilum: MH252535). Introns present in more than 1/5 Basidiomycota species was considered as common introns. The phylogenetic positions of the 75 Basidiomycota species were established using the Bayesian inference (BI) method and Maximum Likelihood (ML) method based on 15 concatenated mitochondrial core proteins and 2 rRNA genes. Species ID are shown in Supplementary Table S1.

FIGURE 8

Mitochondrial gene arrangement analysis of 75 Basidiomycota mitogenomes. 15 core protein coding genes and 2 rRNA genes were included in the gene arrangement, starting from cox1 gene.

FIGURE 9

Molecular phylogeny of 75 Basidiomycota species based on Bayesian inference (BI) and Maximum Likelihood (ML) analyses of 15 protein coding genes and two rRNA genes. Support values are bayesian posterior probabilities (BPP, before slash) and bootstrap values (BS, after slash). The asterisk indicates that the BPP and BS values are 1 and 100, respectively. Species and NCBI accession numbers for genomes used in the phylogenetic analysis are provided in Supplementary Table S1.