Figure 1.
Ideogram of mitochondrial genome of Ganoderma lucidum.
Genes indicated by closed boxes on the outside of the circle are located on the positive strand, whereas those on the inside (orf1, orf2, and trnW) of the circle are located on the negative strand. The genome coordinates and GC contents are shown in the inner circle. The genes are colored based on the functional group they belong. The color scheme is shown in the middle of the circle. Four intron proteins, namely, ip1, ip2, ip3, and ip4, are drawn within the corresponding genes. Four putative clusters of tRNA genes are indicated with brackets and Roman numerals. For clarity, tRNA genes, which are present as isoforms, are indicated by attaching the anticodon to the gene name.
Table 1.
Genetic contents in the mitochondrial genome of Ganoderma lucidum.
Table 2.
Introns found in mitochondrial genes.
Table 3.
Codon usage and codon-anticodon recognition pattern for tRNA in the mitochondrial genome of Ganoderma lucidum.
Table 4.
Distribution of large repeat loci in the mitochondrial genome of Ganoderma Lucidum.
Figure 2.
Similarity analysis of sequences between mtDNA and nuclear DNA.
The top sequence represents the scaffold 48 from the nuclear genome assembly galu96 and the bottom sequence represents the mitochondrion. The homologous regions can be classified into three regions, namely, R1 (white box), R2 (green box), and R3 (blue box), which are connected with black lines at both ends of the corresponding fragments. The coordinates showing the start and end of each region are also shown. F1 and F3 represent two forward repeats. Endonuclease gene and atp6 are also indicated (red box) in GaLu96_scf48.
Figure 3.
Mitochondrial transcriptome of Ganoderma lucidum in three differential developmental stages.
Red and blue colors indicate that the genes or reads are on the forward and reverse strands, respectively. (A) Genome organization of G. lucidum mitochondria. The intron and exon structures of genes, as well as the names of genes, are shown. Two TAR regions, namely, TAR1 and TAR2, are shown. The mapping of RNA-Seq reads from mycelia (B), primordia (C), and fruiting bodies (D) is also shown. The nucleotide coordinates are shown at the very bottom of the figure.
Figure 4.
Mitochondrial gene expressions.
A. Graphic representation of mRNA abundance for the indicated genes at differential stages analyzed by RNA-Seq. B. Graphic representation of mRNA abundance for the indicated genes at differential stages, as measured by RT-qPCR or RNA-Seq. Error bars denote the standard deviation of the three RT-qPCR replicates. C. Hierarchical clustering of mitochondrial gene expression across three different developmental stages: mycelia, primordia, and fruiting bodies.
Table 5.
Identification of RNA-editing sites.
Figure 5.
Molecular phylogenetic analysis.
Amino acid sequences of the genes atp6, atp8, atp9, cob, cox1, and cox2 in Ganoderma lucidum and other 16 fungal species were used to construct this tree with the maximum likelihood method implemented in the software MEGA 5.05. The order, sub-kingdom, and kingdom corresponding to each species show their taxonomic classifications. Bootstrap supports were calculated from 1000 replicates.
Figure 6.
Synteny analysis of mitochondrial genomes.
Synteny comparison of genomes between Ganoderma lucidum and Trametes cingulata (A), Schizophyllum commune (B), Cryptococcus neoformans (C), and Ustilago maydis (D). The genes are represented with lines, and their names are shown next to the corresponding lines. The conserved gene blocks are highlighted with parentheses. The conserved regions are bridged by lines. Genome synteny visualization was performed by GSV, a web-based genome synteny viewer. Co-rearrangement genes are underlined.