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Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829 Cologne, Germany
INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
Department of Biological Sciences, King Abdulaziz University, Jeddah 999088, Saudi Arabia
Department of Microbial and Plant Biology, University of California Berkeley, Berkeley, CA 94720, USA
Authors to whom correspondence should be addressed.
Academic Editors: Yang Xiao and László Nagy
J. Fungi 2022, 8(3), 311;
Received: 8 February 2022 / Revised: 16 March 2022 / Accepted: 16 March 2022 / Published: 18 March 2022
(This article belongs to the Special Issue Genomics and Evolution of Macrofungi)
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species. View Full-Text
Keywords: Ganoderma; genomics; secondary metabolism; secretome; terpenes; wood decay Ganoderma; genomics; secondary metabolism; secretome; terpenes; wood decay
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MDPI and ACS Style

Sun, Y.-F.; Lebreton, A.; Xing, J.-H.; Fang, Y.-X.; Si, J.; Morin, E.; Miyauchi, S.; Drula, E.; Ahrendt, S.; Cobaugh, K.; Lipzen, A.; Koriabine, M.; Riley, R.; Kohler, A.; Barry, K.; Henrissat, B.; Grigoriev, I.V.; Martin, F.M.; Cui, B.-K. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J. Fungi 2022, 8, 311.

AMA Style

Sun Y-F, Lebreton A, Xing J-H, Fang Y-X, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, Lipzen A, Koriabine M, Riley R, Kohler A, Barry K, Henrissat B, Grigoriev IV, Martin FM, Cui B-K. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. Journal of Fungi. 2022; 8(3):311.

Chicago/Turabian Style

Sun, Yi-Fei, Annie Lebreton, Jia-Hui Xing, Yu-Xuan Fang, Jing Si, Emmanuelle Morin, Shingo Miyauchi, Elodie Drula, Steven Ahrendt, Kelly Cobaugh, Anna Lipzen, Maxim Koriabine, Robert Riley, Annegret Kohler, Kerrie Barry, Bernard Henrissat, Igor V. Grigoriev, Francis M. Martin, and Bao-Kai Cui. 2022. "Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species" Journal of Fungi 8, no. 3: 311.

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