Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length

作者：Fei Liu, Xiaomei Ma, Bei Han, Bo Wang, Jianping Xu, Bin Cao, Zhi-Lin Ling, Mao-Qiang He, Xin-Yu Zhu, Rui-Lin Zhao · 发表于：Journal of Advanced Research · 年份：2024 · DOI：10.1016/j.jare.2024.11.005 · 被引用次数：20 · 研究领域：Fungal Biology and Applications、Silymarin and Mushroom Poisoning、Mycorrhizal Fungi and Plant Interactions

• 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 ...