Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication

Abstract

In order to reveal the genetic variation signals of Auricularia heimuer that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of A. heimuer 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 ahchi1 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 ahchi1 gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the ahchi1 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 ahchi1 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 ahchi1 gene in domestication, thereby providing a foundation for elucidating the potential function of the ahchi1 gene in the breeding of A. heimuer.

Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research Techniques, Functional Analysis, and Prospects

“…They further revealed the dynamics of the toxin gene in natural evolution, providing an effective pathway for exploring secondary metabolites in other Basidiomycota. The pangenome of Auricularia heimuer constructed by Guo et al [17] included 14,089 gene families, 67.56% of which were core gene families and 31.88% of which were minor gene families. The genome was screened for the chitinase gene ahchi1 and a carbohydrate-binding module (CBM)-related gene, which provided a reference for genes related to substrate utilization in edible and medicinal fungi.…”