Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length
Fei Liu, Xiaomei Ma, Bei Han, Bo Wang, Jianping Xu, Bin Cao, Zhi-Lin Ling, Mao-Qiang He, Xin-Yu Zhu, Rui-Lin Zhao
Abstract
• Analyzed 199 wild and cultivated strains of Flammulina filiformis . • Identified four distinct populations related to artificial selection intensity. • Cultivated strains showed reduced genome size, gene number, and genetic diversity. • Lost genes during domestication increased disease susceptibility in cultivated strains. • Four genes linked to cap color identified; two confirmed by genetic transformation. • PAV variation played a crucial role in domestication, affecting cap color and stalk length. The 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. This 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. We 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 stalk length. Gene functional confirmation was achieved through genetic transformation experiments. Our 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. This study uncovered significant genomic variations between cultivated and wild Flammulina 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.