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

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-635) contains supplementary material, which is available to authorized users.

Biocatalytic portfolio of Basidiomycota

“…Several catalytically versatile cytochrome P450 (CYP) families such as CYP63 and CYP5144 are enriched in most Basidiomycota and are presumed to participate in the degradation of xenobiotic compounds [27,29,55]. CYP5144 members are also frequently found in secondary metabolic gene clusters [12,55], including sesquiterpenoid gene clusters described by us [13,28,56]. Other CYP families (e.g.…”

“…CYP5348, CYP5359) have been expanded in a species specific manner, probably as an adaptation to specific ecological niches. Members of several of these CYP families have been shown to oxidize diverse compounds including various hydrocarbons, plant metabolites, pharmaceuticals and steroids [12,55]. A genome-wide functional screening in S. cerevisiae was carried out with a total of 300 P450s amplified from cDNA of the brown rotter Postia placenta and white rotter Phanerochaete chrysosporium [57,58].…”

Cloning, overexpression, purification, and modeling of a lectin (Rhinocelectin) with antiproliferative activity from Tiger Milk Mushroom, Lignosus rhinocerus

“…The genome of L. rhinocerus encodes for nine putative lectins, two putative fungal immunomodulatory proteins (FIP) and four putative laccases . Taking advantage of the available genome databases (NCBI nr Fungi and L. rhinocerus ), a number of the proteins have been identified .…”

“…15 The genome of L. rhinocerus encodes for nine putative lectins, two putative fungal immunomodulatory proteins (FIP) and four putative laccases. 16 Taking advantage of the available genome databases (NCBI nr Fungi and L. rhinocerus), a number of the proteins have been identified. 17 Of the 45 major protein spots on 2D gel profile of L. rhinocerus aqueous extract examined using MALDI-MS, 16 are putative lectins from three isoforms encoded as GME270 (180 amino acids), GME272 (173 amino acids), and GME273 (598 amino acids).…”

“…16 Taking advantage of the available genome databases (NCBI nr Fungi and L. rhinocerus), a number of the proteins have been identified. 17 Of the 45 major protein spots on 2D gel profile of L. rhinocerus aqueous extract examined using MALDI-MS, 16 are putative lectins from three isoforms encoded as GME270 (180 amino acids), GME272 (173 amino acids), and GME273 (598 amino acids). They account for up to 39.13% of the major soluble protein constituents of the sclerotium based on the predicted open reading frames of L. rhinocerus genome.…”