The Genome of the Medicinal Macrofungus Sanghuang Provides Insights Into the Synthesis of Diverse Secondary Metabolites

Abstract

The mushroom, Sanghuang is widely used in Asian countries. This medicinal fungus produces diverse bioactive compounds and possesses a potent ability to degrade the wood of the mulberry tree. However, the genes, pathways, and mechanisms that are involved in the biosynthesis of the active compounds and wood degradation by Sanghuang mushroom are still unknown. Here, we report a 34.5 Mb genome-encoding 11,310 predicted genes-of this mushroom. About 16.88% (1909) of the predicted genes have been successfully classified as EuKaryotic Orthologous Groups, and approximately 27.23% (665) of these genes are involved in metabolism. Additionally, a total of 334 genes encoding CAZymes-and their characteristics-were compared with those of the other fungi. Homologous genes involved in triterpenoid, polysaccharide, and flavonoid biosynthesis were identified, and their expression was examined during four developmental stages, 10 and 20 days old mycelia, 1 year old and 3 years old fruiting bodies. Importantly, the lack of chalcone isomerase 1 in the flavonoid biosynthesis pathway suggested that different mechanisms were used in this mushroom to synthesize flavonoids than those used in plants. In addition, 343 transporters and 4 velvet family proteins, involved in regulation, uptake, and redistribution of secondary metabolites, were identified. Genomic analysis of this fungus provides insights into its diverse secondary metabolites, which would be beneficial for the investigation of the medical applications of these pharmacological compounds in the future.

Keywords: CAZymes; Sanghuang; bioactive compound biosynthesis; genomics; transporters.

FIGURE 1

Phylogeny of Sanghuangporus sanghuang strains and selected representative fungi inferred from ITS sequences. Bootstrap values from maximum likelihood analysis. The newly generated sequences for this study have been submitted to GenBank with accession numbers (MN242716–MN242721). The underlined species name was genome-sequenced in this study.

FIGURE 2

Growth characteristics and general genomic features of S. sanghuang Kangneng. (A) The four developmental stages in the life cycle of the fungus. M, aerial mycelia; OY, one-year-old fruiting bodies; TwoY, two-year-old fruiting bodies; ThrY, three-year-old fruiting bodies. Bar = 3 cm. (B) Characteristics of the de novo assembly genomic features. From the outside to the inside are: I, scaffolds, the different colors represent different scaffolds (scaffolds length > 1 Mbp were chosen); II, gene density; III, the density of non-coding RNA; IV, percentage of coverage of repetitive sequences; V, GC content estimated by the percentage of G + C in 20 kb; VI, GC skew was estimated with (G–C)/(G + C) in 20 kb. (C) Genomic element density.

FIGURE 3

KOG functional classification of proteins in the S. sanghuang Kangneng genome.

FIGURE 4

Comparative analysis of CAZymes from S. sanghuang Kangneng and other fungi. (A) Comparative analysis of fungal CAZymes. The numbers of CAZyme modules or domains are represented as horizontal bars. (B) Average number of CAZymes from a total of 30 Basidiomycota fungi. Blue, CAZyme present in other Basidiomycota fungi but not in SSKN; Red, number of CAZymes present in SSKN greater than one-fold the average number of other Basidiomycota fungi; Yellow, CAZymes only present in SSKN. SSKN, S. sanghuang Kangneng.

FIGURE 5

KEGG mapping of the terpenoid backbone biosynthesis pathway and differential expression of the enzymes identified in S. sanghuang Kangneng. (A) The red box indicates existing homologous genes of the enzyme. (B) The expression levels of genes in different developmental stages. Different lowercase letters marked on the bars in each graph denote significant differences (P < 0.05).

FIGURE 6

Differential expression of the enzymes involved in polysaccharide and flavonoid biosynthesis identified in S. sanghuang Kangneng. (A) The expression levels of genes involved in polysaccharide biosynthesis in different developmental stages. (B) Putative pathway of flavonoid biosynthesis in S. sanghuang Kangneng. Black box, no homologous gene was found in the fungal genome; ?, unknown reactions in the fungus. (C) The expression levels of genes involved in flavonoid biosynthesis in different developmental stages. Different lowercase letters marked on the bars in each graph denote significant differences (P < 0.05).