Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu

Yang, Qiang; Song, Haiyan; Su, Ge; Wang, Xuncheng; Hu, Haijing; Zhai, Zhijun; Chen, Minghui; Zhou, Jianping; Yin, Hua; Gao, Yang; Hu, Dianming

doi:10.3390/horticulturae11040409

Open AccessArticle

Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu

by

Qiang Yang

^1,2,3,†,

Haiyan Song

^1,2,4,†,

Ge Su

^1,2,3,

Xuncheng Wang

^5,6,

Haijing Hu

^1,2,3,

Zhijun Zhai

^1,2,3,

Minghui Chen

^1,2,3,

Jianping Zhou

^1,2,3,

Hua Yin

^1,2,3

,

Yang Gao

^1,2,3,*

and

Dianming Hu

^1,2,3,*

¹

Bioengineering and Technological Research Center for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China

²

Nanchang Key Laboratory of Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China

³

Jiangxi Provincial Key Laboratory of Excavation and Utilization of Agricultural Microorganisms, Jiangxi Agricultural University, Nanchang 330045, China

⁴

Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Ministry of Education of the People’s Republic of China, Nanchang 330045, China

⁵

Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing 100097, China

⁶

Academy of Agriculture and Forestry Sciences, Beijing 100097, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Horticulturae 2025, 11(4), 409; https://doi.org/10.3390/horticulturae11040409

Submission received: 23 February 2025 / Revised: 4 April 2025 / Accepted: 7 April 2025 / Published: 11 April 2025

(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)

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Abstract

Cyclocybe chaxingu 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 C. chaxingu have been limited by the lack of comprehensive genomic information. In this study, we performed whole-genome sequencing of the type strain JAUCC1847 of C. chaxingu for the first time and conducted extensive genomic and transcriptomic analyses. We assembled a high-quality genome of the C. chaxingu 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 Agrocybe and Stropharia, suggesting a recent common ancestor. The high ANI values between C. chaxingu, Agrocybe chaxingu, and Agrocybe cylindracea 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 C. chaxingu, particularly in lignocellulose degradation. Comprehensive analysis of the A and B mating-type locus in C. chaxingu 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 C. chaxingu, supporting its recognition within the genus Cyclocybe and providing a valuable resource for future research and breeding programs.

Keywords: Cyclocybe chaxingu; genome; CAZymes; mating-type locus; transcriptomics

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MDPI and ACS Style

Yang, Q.; Song, H.; Su, G.; Wang, X.; Hu, H.; Zhai, Z.; Chen, M.; Zhou, J.; Yin, H.; Gao, Y.; et al. Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu. Horticulturae 2025, 11, 409. https://doi.org/10.3390/horticulturae11040409

AMA Style

Yang Q, Song H, Su G, Wang X, Hu H, Zhai Z, Chen M, Zhou J, Yin H, Gao Y, et al. Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu. Horticulturae. 2025; 11(4):409. https://doi.org/10.3390/horticulturae11040409

Chicago/Turabian Style

Yang, Qiang, Haiyan Song, Ge Su, Xuncheng Wang, Haijing Hu, Zhijun Zhai, Minghui Chen, Jianping Zhou, Hua Yin, Yang Gao, and et al. 2025. "Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu" Horticulturae 11, no. 4: 409. https://doi.org/10.3390/horticulturae11040409

APA Style

Yang, Q., Song, H., Su, G., Wang, X., Hu, H., Zhai, Z., Chen, M., Zhou, J., Yin, H., Gao, Y., & Hu, D. (2025). Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu. Horticulturae, 11(4), 409. https://doi.org/10.3390/horticulturae11040409

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Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu

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