Ganoderma

ARTICLE
Received 2 Feb 2012 | Accepted 22 May 2012 | Published 26 Jun 2012
DOI: 10.1038/ncomms1923

Genome sequence of the model medicinal mushroom Ganoderma lucidum
Shilin Chen1,*, Jiang Xu1,*, Chang Liu1,*, Yingjie Zhu1, David R. Nelson2, Shiguo Zhou3, Chunfang Li1, Lizhi Wang1, Xu Guo1, Yongzhen Sun1, Hongmei Luo1, Ying Li1, Jingyuan Song1, Bernard Henrissat4, Anthony Levasseur5, JunQian1, Jianqin Li1, Xiang Luo1, Linchun Shi1, Liu He1, Li Xiang1, Xiaolan Xu1, Yunyun Niu1, Qiushi Li1, Mira V. Han6, Haixia Yan1, Jin Zhang1, Haimei Chen1, Aiping Lv7, Zhen Wang1, Mingzhu Liu1, David C. Schwartz3 & Chao Sun1

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. Inall, 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 metabolicpathways and their regulation in medicinal fungi.

1 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. 2 Department of

Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA. 3 Laboratory for Molecular and Computational Genomics, Department ofChemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA. 4 Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France. 5 INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, ESIL, 163 Avenue de Luminy, CP 925,13288 Marseille Cedex 09, France. 6 National Evolutionary Synthesis Center, 2024 W. Main Street A200, Durham, North Carolina 27705, USA. 7 China Academy of Chinese Medical Sciences, Beijing 100700, China. *These authors contributed equally to this work. Correspondence and requests for materials should be addressed to S.C. (email: slchen@implad.ac.cn) or to C.S. (email: sunchao_1972@hotmail.com).NATURE COMMUNICATIONS | 3:913 | DOI: 10.1038/ncomms1923 | www.nature.com/naturecommunications

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ARTICLE
anoderma lucidum, also known as ‘the mushroom of immortality’ and ‘the symbol of traditional Chinese medicine’, is one of the best-known medicinal macrofungi in the world. Its pharmacological activities are widely recognized, asindicated by its inclusion in the American Herbal Pharmacopoeia and Therapeutic Compendium1. Modern pharmacological research has demonstrated that G. lucidum exhibits multiple therapeutic activities, including antitumour, antihypertensive, antiviral and immunomodulatory activities2. G. lucidum produces a large reservoir of bioactive compounds; thus far, more than 400 different compounds have beenidentified3, making this fungus a virtual cellular ‘factory’ for biologically useful compounds. Triterpenoids and polysaccharides are the two major categories of pharmacologically active compounds in G. lucidum. In addition to producing these bioactive chemical compounds, G. lucidum, like other white rot basidiomycetes, secretes enzymes that can effectively decompose both cellulose and lignin....