Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

Abstract

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

Keywords: Ganoderma; genomics; secondary metabolism; secretome; terpenes; wood decay.

Figure 1

Comparison of the genome size among the 58 selected species. Bars represent size of 58 genomes and boxplots show proportion of genome size in different lifestyles. The new genomes are shown in red.

Figure 2

ML analyses of 12 Ganoderma strains based on ITS sequences. ML bootstrap values higher than 50% are shown. Stains with sequenced genomes are shown in bold.

Figure 3

Phylogenetic relationship within the Ganoderma clade and 58 selected Basidiomycota species. The ‘best tree’ resulting from maximum likelihood (ML) analyses based on 143 single-copy genes and ML bootstrap values are shown. Colors are coded for the five lifestyles.

Figure 4

(A) Distribution and coverage of transposable elements (TEs) identified in the 58 selected genomes. The bubble size is proportional to the coverage of each of transposable elements (shown inside the bubbles). The bars on top show the total coverage per genome. (B) The copy number of transposable elements (TEs) identified in the 58 genomes. The bubble size is proportional to TE copy number (shown inside the bubbles). The bars on top show the total copy number per genome. Color codes for the five fungal lifestyles are shown at the bottom of the figure.

Figure 5

Presence and abundance of the gene clusters involved in secondary metabolite biosynthesis along with the species phylogenetic relationship between the 58 selected fungal species. The heatmap depicts the number of the gene clusters according to the color scale from blue to red. Color codes for the five fungal lifestyles are shown at the top left of the figure.

Figure 6

Distribution and abundance of the top 100 Pfam protein domains in the selected 58 species. The heatmap depicts the protein domain copy number according to the color scale from purple to green. Color codes for the five fungal lifestyles are shown at the top left of the figure.

Figure 7

Distribution of predicted secreted proteins (i.e., secretome) in Ganoderma species and other selected fungi. Bars represent the gene copy number for CAZymes, lipases, proteases, and SSPs. Color codes for the five fungal lifestyles are shown at the top left of the figure.

Figure 8

Distribution of small secreted proteins (SSPs) in Ganoderma species and other selected fungi. Bars represent the number of annotated (CAZymes, lipases, proteases) and other SSPs. All species are annotated by five lifestyles.

Figure 9

Distribution of secreted CAZymes involved in plant and microbial cell wall degradation in Ganoderma species and other selected fungal genomes. The bubble size is proportional to the number of secreted CAZymes grouped for 11 categories. Colors are coded by five lifestyles. The bar plots show the count of genes involved in PCWDE and MCWDE (left), and the ratio of PCWDE to MCWDE (right).