| Summary: | In order to reveal the genetic variation signals of <i>Auricularia heimuer</i> that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of <i>A. heimuer</i> representing four cultivated strains and four wild strains. The pan-genome contained 14,089 gene families, of which 67.56% were core gene families and 31.88% were dispensable gene families. We screened substrate utilization-related genes such as the chitinase gene <i>ahchi1</i> of the glycoside hydrolase (GH) 18 family and a carbohydrate-binding module (CBM)-related gene from the dispensable families of cultivated populations. The genomic difference in the <i>ahchi1</i> gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the <i>ahchi1</i> gene was 93.75% in the cultivated population, significantly higher than that in the wild population (17.39%), indicating that it has been selected in cultivated strains. Principal component analysis (PCA) of the polymorphic markers in fragments near the <i>ahchi1</i> gene was enriched in cultivated strains, and this was caused by multiple independent instances of artificial selection. We revealed for the first time the genetic basis of the <i>ahchi1</i> gene in domestication, thereby providing a foundation for elucidating the potential function of the <i>ahchi1</i> gene in the breeding of <i>A. heimuer</i>.
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