Genome sequence of the model medicinal mushroom Ganoderma lucidum

Abstract

Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.

Figure 1. An ideogram showing the genomic features of G. lucidum.

(a) GC content was calculated as the percentage of G+C in 100-kb non-overlapping windows. (b) Gene density is represented as the number of genes in 100-kb non-overlapping windows. The intensity of the blue colour correlates with gene density. (c) Pseudochromosome: the diagram represents 13 G. lucidum pseudochromosomes. (d) Genome duplication: regions sharing more than 90% sequence similarity over 5 kb are connected by grey lines; those with more than 90% similarity over 10 kb are connected by orange lines (Supplementary Note 6).

Figure 2. Variations in gene expression and triterpenoid content across the developmental stages of G. lucidum.

Samples from each of the three developmental stages were ground in liquid nitrogen. Half of each sample was used for RNA extraction, and the other half was used for chemical profiling. (a) The three developmental stages in the life cycle of G. lucidum (aerial mycelia of dikaryons, primordia and fruiting bodies) from which samples for gene expression profiling and chemical profiling were collected. (b) Venn diagrams depicting the genes expressed across the different developmental stages. (c) The distribution of gene expression regulation during the stage transitions from mycelia to primordia (T1) and from primordia to fruiting bodies (T2). The x-axis represents the number of genes, and the y-axis represents the log (fold change) for each gene. The distributions of the actual data points are shown on the right sides of panels T1 and T2. The boxes indicate the means (the line in the middle) and the s.d. of the log (fold changes) (from the middle line to the upper and lower edges of the box). (d) HPLC analyses of the triterpenoid contents in the different developmental stages. Three standard compounds are shown: ganoderic acid B (1), ganoderic acid A (2) and ganoderic acid H (3).

Figure 3. CYP gene expression at different developmental stages and phylogenetic analysis coexpressed with LSS.

(a) Two-way clustering of gene-expression profiles for the CYP genes expressed across three developmental stages: mycelia (M), primordial (P) and fruiting bodies (F), as quantified by real-time PCR. The relative expression level of each gene was centred on the mean and then unit scaled across the developmental stages. The floor (shown in green) and ceiling (shown in red) of the expression levels were set as twice the s.d. (b) The phylogenetic analysis of CYPs coexpressed with LSS in G. lucidum (GL) and their homologues in Polyporales. A total of 78 coexpressed CYPs from 21 families in G. lucidum and CYPs from the same families in P. placenta (PP) and P. chrysosporium (PC) were included in the tree. The minimal evolution tree was generated with a heuristic search using the Close-Neighbour-Interchange (CNI) algorithm in MEGA (version 5.05). Bootstrap values based on 1,000 replications was set and shown between 50 and 100 just as the branch colours changed from blue, black to red. Moreover, the genes from the same family or subfamily were collapsed and shown as triangles.

Figure 4. Putative CYP gene clusters found in the G. lucidum genome.

The genes are represented by lines on the chromosomal fragments. The colours of the lines indicate whether the genes are in the forward (blue) or reverse (red) orientation. The beginning and end of each cluster is shown to the left, and each cluster is labelled according to the CYP genes it contains. The chromosome numbers are shown at the top.