The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties

Abstract

Background: The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties.

Results: The de novo assembled 34.3 Mb L. rhinocerotis genome encodes 10,742 putative genes with 84.30% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship of L. rhinocerotis to Ganoderma lucidum, Dichomitus squalens, and Trametes versicolor in the core polyporoid clade. The L. rhinocerotis genome encodes a repertoire of enzymes engaged in carbohydrate and glycoconjugate metabolism, along with cytochrome P450s, putative bioactive proteins (lectins and fungal immunomodulatory proteins) and laccases. Other genes annotated include those encoding key enzymes for secondary metabolite biosynthesis, including those from polyketide, nonribosomal peptide, and triterpenoid pathways. Among them, the L. rhinocerotis genome is particularly enriched with sesquiterpenoid biosynthesis genes.

Conclusions: The genome content of L. rhinocerotis provides insights into the genetic basis of its reported medicinal properties as well as serving as a platform to further characterize putative bioactive proteins and secondary metabolite pathway enzymes and as a reference for comparative genomics of polyporoid fungi.

Figure 1

Various stages of L. rhinocerotis development. (A) Culture of L. rhinocerotis mycelium on nutrified agar, also known as the “Tiger-Eyes” (2 weeks culture). (B) Mycelial cultures of L. rhinocerotis on solid medium (1 to 2 months cultures). (C) Newly formed sclerotia on the surface of culture medium (4 to 6 months culture). (D) L. rhinocerotis sclerotia, the part with medicinal value. (E) Fruiting body of L. rhinocerotis with pileus (cap) and stipe (stalk) attached to the sclerotium.

Figure 2

KOG classification of proteins in L. rhinocerotis . Distribution of predicted proteins from L. rhinocerotis genome according to functional class by Eukaryotic Clusters of Orthologs (KOG) database.

Figure 3

GO and KEGG classifications of proteins in L. rhinocerotis . Distribution of predicted proteins from L. rhinocerotis genome by (A) Gene Ontology (GO) and (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.

Figure 4

Phylogenetic tree of L. rhinocerotis showing the evolutionary distance with different fungal species. Phylogenetic tree construction from a concatenated alignment of 144 shared proteins rooting Saccharomyces cerevisiae as the outgroup. Branch lengths were estimated based on Bayesian inference and all bootstrap values are 100% unless otherwise specified on the lower left side of the internal node(s). Abbreviations: Sac, Saccharomycetales; Eur, Eurotiales; Puc, Pucciniales; Ust, Ustilaginales; Tre, Tremellales; Hym, Hymenochaetales.