Abstract
Agaricus bisporus, one of the most widely cultivated mushrooms around the world, plays an important role in economy and agriculture. In this study, by employing long-reads generated by PacBio and Nanopore sequencing, we assembled six novel high-quality genomes (of which three are telomere-to-telomere assemblies) with sizes 29.6 ~ 30.8 Mb and N50 lengths of 2.5 ~ 2.6 Mb. Combined with public genome data of nine strains, we successfully established a pan-genome of A. bisporus, comprising a total of 14,626 clusters of protein coding genes, of which 50.70%, 7.45%, 24.74% and 17.01% are defined as core, soft core, dispensable, and private clusters, respectively. A total of 5,646 non- redundant structural variants (SVs) were identified among wild and cultivated strains and the genes associated with SV were mapped. This work provides valuable whole-genome sequences and genomic resources across wild and cultivated strains of the most widely cultivated mushroom species for functional analyses of genomes.