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

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Veröffentlicht in:Journal of Fungi vol. 11, no. 9 (2025), p. 647-665
1. Verfasser: Qiao Yanming
Weitere Verfasser: Jia Zhiyuan, Liu, Yuying, Zhang, Na, Luo, Chun, Meng, Lina, Cheng Yajie, Li Minglei, Xie Xiuchao, Jianzhao, Qi
Veröffentlicht:
MDPI AG
Schlagworte:
United States > US
DNA methylation
Software
Glycosides
Phylogenetics
Antiparasitic agents
Population decline
Epigenetics
MicroRNAs
Data processing
Genomes
Metabolism
Genomics
Nucleotide sequence
Genes
Transfer RNA
Evolutionary genetics
Proteins
Glycoside hydrolase
Gene silencing
Germplasm
Chromosomes
Taxonomy
Genomic analysis
Integrated approach
Single-nucleotide polymorphism
Algorithms
Annotations
Haplotypes
Enzymes
Metabolites
Morphology
Conservation
Organic matter
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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.
ISSN:2309-608X
DOI:10.3390/jof11090647
Quelle:Biological Science Database