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

Summary

Researchers sequenced the complete genome of Lei Wan (Gerronema lapidescens), a medicinal mushroom used in Chinese traditional medicine for treating parasites and digestive issues. The study reveals the mushroom’s genetic makeup, including 15,847 genes and over 3 million methylation marks that may control gene expression. They identified 67 gene clusters that could produce medicinal compounds and 521 enzymes for breaking down organic matter. This genetic blueprint will help scientists understand how to cultivate this threatened species sustainably and develop its health benefits.

Background

Gerronema lapidescens (Lei Wan) is a valued medicinal basidiomycete traditionally used in Chinese traditional medicine for antiparasitic and digestive ailments. The species faces severe conservation threats due to unsustainable wild harvesting and lack of reliable cultivation protocols. No comprehensive genomic resources previously existed for this species.

Objective

To present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01 domesticated from the Qinling Mountains. The study aims to elucidate genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit to support future research on medicinal compound biosynthesis and sustainable cultivation.

Results

High-quality 82.23 Mb assembly anchored to 11 chromosomes with 98.4% BUSCO completeness and 46.03% GC content. Annotation predicted 15,847 protein-coding genes with 81.12% functionally assigned. Identified 8.46 million SNPs and 3.25 million methylation events. CAZyme analysis identified 521 enzymes including 211 Glycoside Hydrolases, and 67 biosynthetic gene clusters with predominantly terpene synthases.

Conclusion

This foundational genomic resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, and enzymatic toolkit. The methylation profiling revealed elevated densities on specific chromosomes suggesting roles in gene silencing and environmental adaptation. Findings provide essential data to support development and utilization of G. lapidescens resources for medicinal compound research and sustainable cultivation.
  • Published in:Journal of Fungi,
  • Study Type:Genomic Analysis,
  • Source: PMID: 41003193, DOI: 10.3390/jof11090647
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