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Volume 11
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01

by
Yanming Qiao
1,
Zhiyuan Jia
2,
Yuying Liu
2,3,
Na Zhang
2,
Chun Luo
1,
Lina Meng
1,
Yajie Cheng
1,
Minglei Li
3,
Xiuchao Xie
1,* and
Jianzhao Qi
2,3,*
1
Shaanxi Province Key Laboratory of Bio-Resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
2
Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
3
Center of Edible Fungi, Northwest A&F University, Yangling 712100, China
*
Authors to whom correspondence should be addressed.
J. Fungi 2025, 11(9), 647; https://doi.org/10.3390/jof11090647 (registering DOI)
Submission received: 1 July 2025 / Revised: 20 August 2025 / Accepted: 29 August 2025 / Published: 1 September 2025
Review Reports Versions Notes

Abstract

Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01, domesticated from the Qinling Mountains. A multi-platform sequencing strategy (Illumina and PacBio HiFi) yielded a high-quality 82.23 Mb assembly anchored to 11 chromosomes, exhibiting high completeness (98.4% BUSCO) and 46.03% GC content. Annotation predicted 15,847 protein-coding genes, with 81.12% functionally assigned. Genome-wide analysis identified 8.46 million high-confidence single-nucleotide polymorphisms (SNPs). Notably, methylation profiling revealed 3.25 million methylation events, with elevated densities on chromosomes 4, 9, and 10, suggesting roles in gene silencing and environmental adaptation. Phylogenomic analyses clarified the evolutionary status of G. lapidescens, whilst gene family evolution indicated moderate dynamics reflecting niche adaptation. Carbohydrate-Active enzymes (CAZymes) analysis identified 521 enzymes, including 211 Glycoside Hydrolases (GHs), consistent with organic matter degradation. Additionally, 3279 SSRs were catalogued as molecular markers. This foundational resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit, underpinning future research into medicinal compound biosynthesis, environmental adaptation, germplasm conservation, and sustainable cultivation.
Keywords: Gerronema lapidescens; methylome; medicinal fungi; sclerotium-forming fungi Gerronema lapidescens; methylome; medicinal fungi; sclerotium-forming fungi

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MDPI and ACS Style

Qiao, Y.; Jia, Z.; Liu, Y.; Zhang, N.; Luo, C.; Meng, L.; Cheng, Y.; Li, M.; Xie, X.; Qi, J. The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01. J. Fungi 2025, 11, 647. https://doi.org/10.3390/jof11090647

AMA Style

Qiao Y, Jia Z, Liu Y, Zhang N, Luo C, Meng L, Cheng Y, Li M, Xie X, Qi J. The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01. Journal of Fungi. 2025; 11(9):647. https://doi.org/10.3390/jof11090647

Chicago/Turabian Style

Qiao, Yanming, Zhiyuan Jia, Yuying Liu, Na Zhang, Chun Luo, Lina Meng, Yajie Cheng, Minglei Li, Xiuchao Xie, and Jianzhao Qi. 2025. "The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01" Journal of Fungi 11, no. 9: 647. https://doi.org/10.3390/jof11090647

APA Style

Qiao, Y., Jia, Z., Liu, Y., Zhang, N., Luo, C., Meng, L., Cheng, Y., Li, M., Xie, X., & Qi, J. (2025). The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01. Journal of Fungi, 11(9), 647. https://doi.org/10.3390/jof11090647

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