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Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

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 blue...

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Autores principales: Sun, Yi-Fei, Lebreton, Annie, Xing, Jia-Hui, Fang, Yu-Xuan, Si, Jing, Morin, Emmanuelle, Miyauchi, Shingo, Drula, Elodie, Ahrendt, Steven, Cobaugh, Kelly, Lipzen, Anna, Koriabine, Maxim, Riley, Robert, Kohler, Annegret, Barry, Kerrie, Henrissat, Bernard, Grigoriev, Igor V., Martin, Francis M., Cui, Bao-Kai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8955403/
https://www.ncbi.nlm.nih.gov/pubmed/35330313
http://dx.doi.org/10.3390/jof8030311
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author Sun, Yi-Fei
Lebreton, Annie
Xing, Jia-Hui
Fang, Yu-Xuan
Si, Jing
Morin, Emmanuelle
Miyauchi, Shingo
Drula, Elodie
Ahrendt, Steven
Cobaugh, Kelly
Lipzen, Anna
Koriabine, Maxim
Riley, Robert
Kohler, Annegret
Barry, Kerrie
Henrissat, Bernard
Grigoriev, Igor V.
Martin, Francis M.
Cui, Bao-Kai
author_facet Sun, Yi-Fei
Lebreton, Annie
Xing, Jia-Hui
Fang, Yu-Xuan
Si, Jing
Morin, Emmanuelle
Miyauchi, Shingo
Drula, Elodie
Ahrendt, Steven
Cobaugh, Kelly
Lipzen, Anna
Koriabine, Maxim
Riley, Robert
Kohler, Annegret
Barry, Kerrie
Henrissat, Bernard
Grigoriev, Igor V.
Martin, Francis M.
Cui, Bao-Kai
author_sort Sun, Yi-Fei
collection PubMed
description 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.
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spelling pubmed-89554032022-03-26 Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species Sun, Yi-Fei Lebreton, Annie Xing, Jia-Hui Fang, Yu-Xuan Si, Jing Morin, Emmanuelle Miyauchi, Shingo Drula, Elodie Ahrendt, Steven Cobaugh, Kelly Lipzen, Anna Koriabine, Maxim Riley, Robert Kohler, Annegret Barry, Kerrie Henrissat, Bernard Grigoriev, Igor V. Martin, Francis M. Cui, Bao-Kai J Fungi (Basel) Article 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. MDPI 2022-03-18 /pmc/articles/PMC8955403/ /pubmed/35330313 http://dx.doi.org/10.3390/jof8030311 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sun, Yi-Fei
Lebreton, Annie
Xing, Jia-Hui
Fang, Yu-Xuan
Si, Jing
Morin, Emmanuelle
Miyauchi, Shingo
Drula, Elodie
Ahrendt, Steven
Cobaugh, Kelly
Lipzen, Anna
Koriabine, Maxim
Riley, Robert
Kohler, Annegret
Barry, Kerrie
Henrissat, Bernard
Grigoriev, Igor V.
Martin, Francis M.
Cui, Bao-Kai
Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title_full Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title_fullStr Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title_full_unstemmed Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title_short Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
title_sort phylogenomics and comparative genomics highlight specific genetic features in ganoderma species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8955403/
https://www.ncbi.nlm.nih.gov/pubmed/35330313
http://dx.doi.org/10.3390/jof8030311
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