Genome sequence of the model medicinal mushroom Ganoderma lucidum

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

doi:10.1038/ncomms1923

Cited by 475 publications

(483 citation statements)

References 60 publications

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“…In addition, we found many hits in the mevalonate branch of the terpenoid backbone biosynthesis pathway. This result is similar to that of G. lucidum (26,27), except for some enzymes downstream of the geranyl diphosphate synthase (GPP) and farnesyl diphosphate synthase (FPP) biosynthesis steps. We also found genes encoding components in the biosynthesis pathways of terpenoid backbone, sesquiterpenoid, ubiquinone, and other terpenoid quinones (SI Appendix, Table S7 and Dataset S1).…”

Section: Resultssupporting

confidence: 76%

Genomic and transcriptomic analyses of the medicinal fungusAntrodia cinnamomeafor its metabolite biosynthesis and sexual development

Fan

Wang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Antrodia cinnamomea, a polyporus mushroom of Taiwan, has long been used as a remedy for cancer, hypertension, and hangover, with an annual market of over $100 million (US) in Taiwan. We obtained a 32.15-Mb genome draft containing 9,254 genes. Genome ontology enrichment and pathway analyses shed light on sexual development and the biosynthesis of sesquiterpenoids, triterpenoids, ergostanes, antroquinonol, and antrocamphin. We identified genes differentially expressed between mycelium and fruiting body and 242 proteins in the mevalonate pathway, terpenoid pathways, cytochrome P450s, and polyketide synthases, which may contribute to the production of medicinal secondary metabolites. Genes of secondary metabolite biosynthetic pathways showed expression enrichment for tissuespecific compounds, including 14-α-demethylase (CYP51F1) in fruiting body for converting lanostane to ergostane triterpenoids, coenzymes Q (COQ) for antroquinonol biosynthesis in mycelium, and polyketide synthase for antrocamphin biosynthesis in fruiting body. Our data will be useful for developing a strategy to increase the production of useful metabolites.medicinal fungus | fruiting body | triterpenes | meiosis | P450

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Section: Resultssupporting

confidence: 76%

Genomic and transcriptomic analyses of the medicinal fungusAntrodia cinnamomeafor its metabolite biosynthesis and sexual development

Fan

Wang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Mycorrhizal fungi depend largely on their plant symbionts for their carbon source (76), and thus, they have a less extensive CAZyme arsenal than the wood-rotting and litter-and straw-decomposing fungi (7,9,72,73). The limited plant-polysaccharidedegrading capability of ECM fungi is a result of evolutionary reduction in CAZyme families (7,71) to suit their role as root symbionts.…”

Section: Ectomycorrhizal Fungimentioning

confidence: 99%

“…However, these methods are laborious and cannot provide a full overview of a fungal CAZyme arsenal. More detailed insights into the entire polysaccharide-degrading capability of fungi with interesting ecologies have been obtained through genome sequencing (6)(7)(8)(9)(10)(11)(12)(13)(14)(15) together with transcriptome and proteome analyses (16)(17)(18). However, only by combining these omics data with biochemical characteristics of the enzymes can we complete our understanding of the plant cell wall polysaccharide degradation ability of basidiomycete fungi.…”

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confidence: 99%

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

Rytioja

Hildén

Yuzon

et al. 2014

Microbiol Mol Biol Rev

355

287

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SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus , to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.

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“…In addition, G. lucidum, like other white rot Basidiomycetes, produces enzymes that can effectively degrade both lignin and cellulose (Ko et al 2001). The transcriptome of G. lucidum fruiting bodies, which are the major medicinal fungal structures used in traditional Chinese medicine, is well annotated and functionally characterized Chen et al 2012;Yu et al 2012). Therefore, characterization of RNA editing in fruiting bodies will greatly augment our understanding of genetic and metabolic diversity and regulation in G. lucidum.…”

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confidence: 99%

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

et al. 2014

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RNA editing is a widespread, post-transcriptional molecular phenomenon that diversifies hereditary information across various organisms. However, little is known about genome-scale RNA editing in fungi. In this study, we screened for fungal RNA editing sites at the genomic level in Ganoderma lucidum, a valuable medicinal fungus. On the basis of our pipeline that predicted the editing sites from genomic and transcriptomic data, a total of 8906 possible RNA-editing sites were identified within the G. lucidum genome, including the exon and intron sequences and the 59-/39-untranslated regions of 2991 genes and the intergenic regions. The major editing types included C-to-U, A-to-G, G-to-A, and U-to-C conversions. Four putative RNA-editing enzymes were identified, including three adenosine deaminases acting on transfer RNA and a deoxycytidylate deaminase. The genes containing RNA-editing sites were functionally classified by the Kyoto Encyclopedia of Genes and Genomes enrichment and gene ontology analysis. The key functional groupings enriched for RNA-editing sites included laccase genes involved in lignin degradation, key enzymes involved in triterpenoid biosynthesis, and transcription factors. A total of 97 putative editing sites were randomly selected and validated by using PCR and Sanger sequencing. We presented an accurate and large-scale identification of RNA-editing events in G. lucidum, providing global and quantitative cataloging of RNA editing in the fungal genome. This study will shed light on the role of transcriptional plasticity in the growth and development of G. lucidum, as well as its adaptation to the environment and the regulation of valuable secondary metabolite pathways. RNA editing is a post-transcriptional process that can enhance the diversity of gene products by altering RNA sequences. This can involve site-specific nucleotide modifications, nucleotide insertions/deletions, and nucleotide substitutions (Gott and Emeson 2000;Bass 2002;Farajollahi and Maas 2010). RNA editing can affect messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs, and small regulatory RNAs present in all cellular compartments and has been described in a wide range of organisms from viruses to fungi, mammals, and plants ( Gott and Emeson 2000;Gott 2003;Kawahara et al. 2007). The prevalent RNA-editing pathways in higher eukaryotes involves the deamination of cytidine (C) to create uridine (U) and deamination of adenosine (A) to create inosine (I) (Bass 2002;Gott 2003). The editing process generally involves a specificity factor (RNA or protein) that recognizes the editing site, as well as an enzyme, occasionally with other accessory factors, that catalyzes the reaction (Bass 2002). The functions of RNA editing include regulation of gene expression, increasing protein diversity and reversion of the effect of mutations in the genome (Gott and Emeson 2000;Gott 2003). In many cases, RNA editing is essential for correcting protein production (Young 1990) or for modulating the functional properties of proteins...

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Genome sequence of the model medicinal mushroom Ganoderma lucidum

Cited by 475 publications

References 60 publications

Genomic and transcriptomic analyses of the medicinal fungusAntrodia cinnamomeafor its metabolite biosynthesis and sexual development

Genomic and transcriptomic analyses of the medicinal fungusAntrodia cinnamomeafor its metabolite biosynthesis and sexual development

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

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