Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny

Abstract

Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.

Keywords: Phallus; gene rearrangement; intron; mitochondrial genome; phylogenetic analysis.

FIGURE 1

Circular maps of the mitogenomes of two Phallus species. The first nt of the cox1 gene was defined as nt 1 of the genome artificially. Various genes are represented with different color blocks.

FIGURE 2

The intronic, intergenic, protein-coding, and RNA gene region proportions of the entire mitogenomes of two Phallus species. The bottom panel shows the contribution of different gene regions to the expansion of the P. indusiatus mitogenome. The value of bar chart is based on the ratio of differences in the protein-coding genes, RNA sequence, intronic region, and intergenic region between P. indusiatus and P. echinovolvatus mitogenomes to the difference of their entire mitogenomes.

FIGURE 3

Variation in the length and base composition of each of 15 protein-coding genes (PCGs) between two Phallus mitogenomes. (A) PCG length variation; (B) GC content of the PCGs; (C) AT skew; (D) GC skew.

FIGURE 4

Genetic analysis of 15 protein-coding genes conserved in two Phallus mitogenomes. K2P, the Kimura-2-parameter distance; Ka, the mean number of non-synonymous substitutions per non-synonymous site; Ks, the mean number of synonymous substitutions per synonymous site.

FIGURE 5

Mitochondrial gene arrangement analyses of 44 Basidiomycete species. Genes are represented with different color blocks. All genes are shown in order of occurrence in the mitochondrial genome, starting from cox1. Fourteen core protein-coding genes, one rps3 gene, and two rRNA genes were included in the gene arrangement analysis. Species and NCBI accession number used for gene arrangement analysis in the present study are listed in Supplementary Table S5.

FIGURE 6

Mitogenome synteny among six Basidiomycetes species. Twenty-three homologs regions (A–Y) were identified among the six mitogenomes. The sizes and relative positions of the homologs fragments varied across the mitogenomes.

FIGURE 7

Position class (Pcl) information of cox1 gene of 44 Basidiomycete species. The same Pcl (orthologs intron) is represented by the same letter. The phylogenetic positions of 44 Basidiomycete species were established using the Bayesian inference (BI) method based on a 14 conserved mitochondrial gene set. N1–N3 represent the newly detected Pcl in this study; II in the figure shows that the intron belongs to group II introns. Species IDs are shown in Supplementary Table S5.

FIGURE 8

Comparison of 15 bp sequence upstream and downstream of the insertion site of Pcl II2. Probable insertion site is shown by the triangle. Asterisks represent base pairs that are in the same corresponding position. Sequences were aligned by Clustal W in MEGA v6.06.

FIGURE 9

Bayesian phylogenies of 44 fungal species using individual genes including each of 14 conserved protein-coding genes. Glarea lozoyensis was used as an outgroup. Support values are Bayesian posterior probabilities. Species and NCBI accession number used for phylogenetic analyses are provided in Supplementary Table S5.