ArticleJournal of advanced research2025
Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length.
Article in Journal of advanced research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
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- Genome-wide association studies revealed association between LePC4 gene and crude protein content in shiitake mushroom, Lentinula edodes.World journal of microbiology & biotechnology · 2026Article
- Assessment of genome evolution inmSystems · 2026Article
- Comparative Mitogenomics Reveals Intron Dynamics and Mitochondrial Gene Expression Shifts in Domesticated and WildJournal of fungi (Basel, Switzerland) · 2026Article
- Molecular mechanisms and horticultural implications of temperature-induced color variation inFood chemistry. Molecular sciences · 2025Article
- Genomic insights and SSR marker development for trait improvement in Pleurotus giganteus for tropical cultivation.BMC plant biology · 2025Article
- High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap MushroomMicroorganisms · 2025Article
- Identification of Critical Candidate Genes Controlling Monokaryon Fruiting inJournal of fungi (Basel, Switzerland) · 2025Article
- Discovery of a New Starship Transposon Driving the Horizontal Transfer of theMicroorganisms · 2025Article
- A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus.Microbial biotechnology · 2025Article
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10 authors.
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Abstract
introductionThe domestication of edible mushrooms, including Flammulina filiformis, offers valuable insights into the genetic changes driven by artificial selection. Understanding these changes is crucial for uncovering the mechanisms behind genome evolution in domesticated mushrooms.
objectivesThis study aims to investigate the population structure, genetic diversity, and domestication-related genomic changes in F. filiformis. By comparing the genome sequences of 199 wild and cultivated strains, we aim to elucidate the impact of domestication on F. filiformis.
methodsWe performed de novo genome assembly and gene-based pan-genome analysis on the 199 strains, which included both wild and cultivated strains. We also conducted genome-wide association studies (GWAS) using presence-absence variation (PAV) and SNP data, combined with RNA sequencing, to identify genes associated with domestication traits, such as cap color and stipe length. Gene functional confirmation was achieved through genetic transformation experiments.
resultsOur analysis grouped the strains into four distinct populations, which correlated with varying intensities of artificial selection. The three cultivated populations exhibited smaller genome sizes, fewer genes, lower genetic variation, reduced gene expression diversity, and lower heterozygosity compared to the wild population. The analysis revealed the loss of genes related to the beta-lactam antibiotic catabolic process and specific MAPK pathway genes during domestication, rendering domesticated strains more susceptible to diseases. Four genes closely associated with cap color and stipe length were identified, but genetic transformation experiments confirmed the functional relevance of only two (FfB and FfD) identified through PAV-based GWAS.
conclusionThis study uncovered significant genomic variations between cultivated and wild F. filiformis populations, including the loss of pathogen resistance genes during domestication. We also identified key genes linked to cap color and stipe length, demonstrating for the first time the important role of PAV variation in mushroom domestication. These insights provide a foundation for future mushroom breeding and evolutionary research.
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