title: Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense.
abstract: Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms.
authors.affiliation: 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Yingjie
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Xu
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Sun
authors.affiliation: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Qian
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Jingyuan
authors.initials: J
authors.lastname: Song
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Luo
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Li
authors.initials: L
authors.lastname: Xiang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Zhichao
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Aijia
authors.initials: A
authors.lastname: Ji
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Lizhi
authors.initials: L
authors.lastname: Wang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Shanfa
authors.initials: S
authors.lastname: Lu
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia, 4072.
authors.forename: Alice
authors.initials: A
authors.lastname: Hayward
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Sun
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Xiwen
authors.initials: X
authors.lastname: Li
authors.affiliation: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China.
authors.forename: Yitao
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Chen
mesh_terms: D002874:Chromosome Mapping; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D032902:Ganoderma / Q000145:classification / Q000235:genetics*; D020868:Gene Silencing; D016681:Genome, Fungal; D005810:Multigene Family; D010802:Phylogeny; D034741:RNA, Small Interfering / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004271:DNA, Fungal; D034741:RNA, Small Interfering