Objective  By resequencing the genomes of representative strains of Agaricus bisporus, the genetic differentiations and molecular markers were investigated for taxonomic and analytical studies on the mushrooms.

  Method  Genes of 18 major strains of A. bisporus including hybrids and wild strains from local and foreign sources, traditional highly productive or good quality varieties, and brown-colored and sterile strains were resequenced. Various bioinformatics software programs were applied to align the readings with the reference A. bisporus genome data. From the aligned results, SNP and SV were obtained to statistically analyze the distribution of the genetic differentiations in search for DNA-based molecular markers and to decipher the functions of the genomes.

  Result  From the resequencing, 21.63 G data were obtained with an average Q30 reaching 89.10%. A matching rate of 82.50%, a coverage of 96.32%, and an average depth of 33X were found between the readings and sequence of the H97 reference genome. From the alignment results, 813 768 SNPs and 53 840 InDels were obtained with an average of 924 SV variations for each strain.

  Conclusion  Of the various A. bisporus strains in the world, the Chinese As2796 and Dutch U1 lines seemed to be the two major commercial hybrids on the market.