Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense

Yingjie Zhu, Jiang Xu, Chao Sun, Shiguo Zhou, Haibin Xu, David Nelson, Jun Qian, Jingyuan Song, Hongmei Luo, Li Xiang, Ying Li, Zhichao Xu, Aijia Ji, Lizhi Wang, Shanfa Lu, Alice Hayward, Wei Sun, Xiwen Li, David C. Schwartz, Yitao Wang & 1 others Shilin Chen

Research output: Contribution to journalArticle

19 Citations (Scopus)

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.

Original languageEnglish (US)
Article number11087
JournalScientific Reports
Volume5
DOIs
StatePublished - Jun 5 2015

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Ganoderma
Fungi
DNA Methylation
Chromosomes
Genome
Secondary Metabolism
Point Mutation
Genome Components
RNA
Genes
Chromosomes, Human, Pair 15
Basidiomycota
DNA Transposable Elements
Genomic Instability
Gene Silencing
Multigene Family
Computational Biology
Transcriptome

All Science Journal Classification (ASJC) codes

  • General

Cite this

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense. / Zhu, Yingjie; Xu, Jiang; Sun, Chao; Zhou, Shiguo; Xu, Haibin; Nelson, David; Qian, Jun; Song, Jingyuan; Luo, Hongmei; Xiang, Li; Li, Ying; Xu, Zhichao; Ji, Aijia; Wang, Lizhi; Lu, Shanfa; Hayward, Alice; Sun, Wei; Li, Xiwen; Schwartz, David C.; Wang, Yitao; Chen, Shilin.

In: Scientific Reports, Vol. 5, 11087, 05.06.2015.

Research output: Contribution to journalArticle

Zhu, Y, Xu, J, Sun, C, Zhou, S, Xu, H, Nelson, D, Qian, J, Song, J, Luo, H, Xiang, L, Li, Y, Xu, Z, Ji, A, Wang, L, Lu, S, Hayward, A, Sun, W, Li, X, Schwartz, DC, Wang, Y & Chen, S 2015, 'Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense', Scientific Reports, vol. 5, 11087. https://doi.org/10.1038/srep11087
Zhu, Yingjie ; Xu, Jiang ; Sun, Chao ; Zhou, Shiguo ; Xu, Haibin ; Nelson, David ; Qian, Jun ; Song, Jingyuan ; Luo, Hongmei ; Xiang, Li ; Li, Ying ; Xu, Zhichao ; Ji, Aijia ; Wang, Lizhi ; Lu, Shanfa ; Hayward, Alice ; Sun, Wei ; Li, Xiwen ; Schwartz, David C. ; Wang, Yitao ; Chen, Shilin. / Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense. In: Scientific Reports. 2015 ; Vol. 5.
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