Genome sequence of the model medicinal mushroom Ganoderma lucidum

Shilin Chen; Jiang Xu; Chang Liu; Yingjie Zhu; David R. Nelson; Shiguo Zhou; Chunfang Li; Lizhi Wang; Xu Guo; Yongzhen Sun; Hongmei Luo; Ying Li; Jingyuan Song; Bernard Henrissat; Anthony Levasseur; Jun Qian; Jianqin Li; Xiang Luo; Linchun Shi; Liu He; Li Xiang; Xiaolan Xu; Yunyun Niu; Qiushi Li; Mira V. Han; Haixia Yan; Jin Zhang; Haimei Chen; Aiping Lv; Zhen Wang; Mingzhu Liu; David C. Schwartz; Chao Sun

doi:10.1038/ncomms1923

Genome sequence of the model medicinal mushroom Ganoderma lucidum

Shilin Chen, Jiang Xu, Chang Liu, Yingjie Zhu, David R. Nelson, Shiguo Zhou, Chunfang Li, Lizhi Wang, Xu Guo, Yongzhen Sun, Hongmei Luo, Ying Li, Jingyuan Song, Bernard Henrissat, Anthony Levasseur, Jun Qian, Jianqin Li, Xiang Luo, Linchun Shi, Liu HeLi Xiang, Xiaolan Xu, Yunyun Niu, Qiushi Li, Mira V. Han, Haixia Yan, Jin Zhang, Haimei Chen, Aiping Lv, Zhen Wang, Mingzhu Liu, David C. Schwartz, Chao Sun

Research output: Contribution to journal › Article › peer-review

283 Scopus citations

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.

Original language	English (US)
Article number	913
Journal	Nature communications
Volume	3
DOIs	https://doi.org/10.1038/ncomms1923
State	Published - 2012
Externally published	Yes

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/ncomms1923

Cite this

Chen, S, Xu, J, Liu, C, Zhu, Y, Nelson, DR, Zhou, S, Li, C, Wang, L, Guo, X, Sun, Y, Luo, H, Li, Y, Song, J, Henrissat, B, Levasseur, A, Qian, J, Li, J, Luo, X, Shi, L, He, L, Xiang, L, Xu, X, Niu, Y, Li, Q, Han, MV, Yan, H, Zhang, J, Chen, H, Lv, A, Wang, Z, Liu, M, Schwartz, DC & Sun, C 2012, 'Genome sequence of the model medicinal mushroom Ganoderma lucidum', Nature communications, vol. 3, 913. https://doi.org/10.1038/ncomms1923

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title = "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.",

author = "Shilin Chen and Jiang Xu and Chang Liu and Yingjie Zhu and Nelson, {David R.} and Shiguo Zhou and Chunfang Li and Lizhi Wang and Xu Guo and Yongzhen Sun and Hongmei Luo and Ying Li and Jingyuan Song and Bernard Henrissat and Anthony Levasseur and Jun Qian and Jianqin Li and Xiang Luo and Linchun Shi and Liu He and Li Xiang and Xiaolan Xu and Yunyun Niu and Qiushi Li and Han, {Mira V.} and Haixia Yan and Jin Zhang and Haimei Chen and Aiping Lv and Zhen Wang and Mingzhu Liu and Schwartz, {David C.} and Chao Sun",

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T1 - Genome sequence of the model medicinal mushroom Ganoderma lucidum

AU - Chen, Shilin

AU - Xu, Jiang

AU - Liu, Chang

AU - Zhu, Yingjie

AU - Nelson, David R.

AU - Zhou, Shiguo

AU - Li, Chunfang

AU - Wang, Lizhi

AU - Guo, Xu

AU - Sun, Yongzhen

AU - Luo, Hongmei

AU - Li, Ying

AU - Song, Jingyuan

AU - Henrissat, Bernard

AU - Levasseur, Anthony

AU - Qian, Jun

AU - Li, Jianqin

AU - Luo, Xiang

AU - Shi, Linchun

AU - He, Liu

AU - Xiang, Li

AU - Xu, Xiaolan

AU - Niu, Yunyun

AU - Li, Qiushi

AU - Han, Mira V.

AU - Yan, Haixia

AU - Zhang, Jin

AU - Chen, Haimei

AU - Lv, Aiping

AU - Wang, Zhen

AU - Liu, Mingzhu

AU - Schwartz, David C.

AU - Sun, Chao

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

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Genome sequence of the model medicinal mushroom Ganoderma lucidum

Abstract

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