Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i>
<i>Cyclocybe chaxingu</i> is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on <i>C. chaxingu</i> have been limited by the lack of comprehensive ge...
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2025-04-01
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| author | Qiang Yang Haiyan Song Ge Su Xuncheng Wang Haijing Hu Zhijun Zhai Minghui Chen Jianping Zhou Hua Yin Yang Gao Dianming Hu |
| author_facet | Qiang Yang Haiyan Song Ge Su Xuncheng Wang Haijing Hu Zhijun Zhai Minghui Chen Jianping Zhou Hua Yin Yang Gao Dianming Hu |
| author_sort | Qiang Yang |
| collection | DOAJ |
| description | <i>Cyclocybe chaxingu</i> is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on <i>C. chaxingu</i> have been limited by the lack of comprehensive genomic information. In this study, we performed whole-genome sequencing of the type strain JAUCC1847 of <i>C. chaxingu</i> for the first time and conducted extensive genomic and transcriptomic analyses. We assembled a high-quality genome of the <i>C. chaxingu</i> strain C27, with a total length of 50.79 Mb and a GC content of 50.90%. Comparative genomic analysis revealed a close evolutionary relationship with species from the genera <i>Agrocybe</i> and <i>Stropharia</i>, suggesting a recent common ancestor. The high ANI values between <i>C. chaxingu</i>, <i>Agrocybe chaxingu</i>, and <i>Agrocybe cylindracea</i> indicate a close phylogenetic relationship, raising the possibility of synonymy among these strains. Genome annotation identified a rich array of 573 carbohydrate-active enzymes, highlighting the metabolic diversity of <i>C. chaxingu</i>, particularly in lignocellulose degradation. Comprehensive analysis of the A and B mating-type locus in <i>C. chaxingu</i> revealed the distribution and structural characteristics of mating-type genes, providing crucial genetic information for further studies on the reproductive biology of this species. Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. GO and KEGG enrichment analyses demonstrated the stipe’s association with structural integrity and transport, while the cap is linked to metabolic activity, gene regulation, stress responses, and DNA repair. These insights clarify the taxonomic status of <i>C. chaxingu</i>, supporting its recognition within the genus <i>Cyclocybe</i> and providing a valuable resource for future research and breeding programs. |
| format | Article |
| id | doaj-art-3e8bf6207b1a4bd2b9f7ee023f2cc097 |
| institution | OA Journals |
| issn | 2311-7524 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
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| series | Horticulturae |
| spelling | doaj-art-3e8bf6207b1a4bd2b9f7ee023f2cc0972025-08-20T02:18:05ZengMDPI AGHorticulturae2311-75242025-04-0111440910.3390/horticulturae11040409Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i>Qiang Yang0Haiyan Song1Ge Su2Xuncheng Wang3Haijing Hu4Zhijun Zhai5Minghui Chen6Jianping Zhou7Hua Yin8Yang Gao9Dianming Hu10Bioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBeijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing 100097, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, ChinaBioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China<i>Cyclocybe chaxingu</i> is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on <i>C. chaxingu</i> have been limited by the lack of comprehensive genomic information. In this study, we performed whole-genome sequencing of the type strain JAUCC1847 of <i>C. chaxingu</i> for the first time and conducted extensive genomic and transcriptomic analyses. We assembled a high-quality genome of the <i>C. chaxingu</i> strain C27, with a total length of 50.79 Mb and a GC content of 50.90%. Comparative genomic analysis revealed a close evolutionary relationship with species from the genera <i>Agrocybe</i> and <i>Stropharia</i>, suggesting a recent common ancestor. The high ANI values between <i>C. chaxingu</i>, <i>Agrocybe chaxingu</i>, and <i>Agrocybe cylindracea</i> indicate a close phylogenetic relationship, raising the possibility of synonymy among these strains. Genome annotation identified a rich array of 573 carbohydrate-active enzymes, highlighting the metabolic diversity of <i>C. chaxingu</i>, particularly in lignocellulose degradation. Comprehensive analysis of the A and B mating-type locus in <i>C. chaxingu</i> revealed the distribution and structural characteristics of mating-type genes, providing crucial genetic information for further studies on the reproductive biology of this species. Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. GO and KEGG enrichment analyses demonstrated the stipe’s association with structural integrity and transport, while the cap is linked to metabolic activity, gene regulation, stress responses, and DNA repair. These insights clarify the taxonomic status of <i>C. chaxingu</i>, supporting its recognition within the genus <i>Cyclocybe</i> and providing a valuable resource for future research and breeding programs.https://www.mdpi.com/2311-7524/11/4/409<i>Cyclocybe chaxingu</i>genomeCAZymesmating-type locustranscriptomics |
| spellingShingle | Qiang Yang Haiyan Song Ge Su Xuncheng Wang Haijing Hu Zhijun Zhai Minghui Chen Jianping Zhou Hua Yin Yang Gao Dianming Hu Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> Horticulturae <i>Cyclocybe chaxingu</i> genome CAZymes mating-type locus transcriptomics |
| title | Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> |
| title_full | Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> |
| title_fullStr | Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> |
| title_full_unstemmed | Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> |
| title_short | Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> |
| title_sort | genomic and transcriptomic analysis to explore the biological characteristics of i cyclocybe chaxingu i |
| topic | <i>Cyclocybe chaxingu</i> genome CAZymes mating-type locus transcriptomics |
| url | https://www.mdpi.com/2311-7524/11/4/409 |
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