Objective  Key genes associated with Agaricus bisporus of different mycelial morphology were analyzed. Methods As 2796, the main cultivated variety of A. bisporus, with aerial or creepy hyphae grown on same plate were collected for RNA transcriptome sequencing and comparison with reference.

Results  There were 965 differentially expressed genes (DEGs) between the aerial hyphae-A601 and the creepy hyphae-A602. According to the GO enrichment analysis, the hydrophobic DEGs were enriched in the fungal cell wall, such as AGABI2DRAFT_13655, AGABI2DRAFT_136569, and AGABI2DRAFT_193057 that belonged to the ABH3 protein gene family, with expressions significantly higher in A601 than in A602. Thus, they were postulated to be related to the production of aerial hyphae. In addition, the hydrophobic surface binding protein A (HsbA)-related gene, AGABI2DRAFT_194662, showed a FPKM expression of 0 in A601, but 10.24 in A602. Furthermore, 8 enriched DEGs related to lipase isoenzymes exhibited a FPKM expression significantly higher in A601 than in A602. The SNP/InDel analysis indicated that the SNPs in A601 was 110 601 as opposed to 111 188 in A602, the most frequent mutation in SNPs was C:G>T:A, and that 2 374 common InDels were identified.

Conclusion  The transcriptomes and possibly associated genes and SNP sites in A. bisporus with different mycelial morphology obtained in this study would be of value for the mushroom germplasm evaluation and breeding.