Open Access Research article

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

Hui-Yeng Y Yap1*, Yit-Heng Chooi2, Mohd Firdaus-Raih3, Shin-Yee Fung1, Szu-Ting Ng4, Chon-Seng Tan5 and Nget-Hong Tan1

Author Affiliations

1 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia

2 Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 0200, Australia

3 School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia

4 Ligno Biotech Sdn. Bhd., 43300 Balakong Jaya, Selangor, Malaysia

5 Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia

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BMC Genomics 2014, 15:635  doi:10.1186/1471-2164-15-635

Published: 29 July 2014

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.

Keywords:
Lignosus rhinocerotis; Genome; Phylogeny; Secondary metabolism; Carbohydrate-active enzymes; Cytochrome P450 superfamily