Integrated transcriptome and DNA methylome analysis reveal the browning mechanism in Agaricus bisporus

The white button mushroom (Agaricus bisporus), widely cultivated worldwide as an edible mushroom, is susceptible to browning, which significantly impacts its nutritional and commercial value. Extensive research has enhanced our understanding of the mechanisms underlying this browning process. Although the role of DNA methylation in regulating gene expression has been studied in many fungi, information specifically concerning DNA methylation during the browning in A. bisporus is still limited. In this study, we initially evaluated the impact of temperatures (4 ℃ and room temperature) on discoloration in A. bisporus, and samples with similar discoloration under different temperatures were collected for transcriptome and DNA methylation sequencing. The results revealed that DNA methylation was positively correlated with browning, suggesting its involvement during the browning in A. bisporus. Further analysis showed the heightened methylation levels were primarily attributed to increased methylation at CHG and CHH sites. By joint analysis of transcriptome and DNA methylome, 342 genes with significant expression changes were identified to be affected by DNA methylation, and finally 13 genes were considered as important browning genes under different signaling pathways, such as ABA/ET pathway. Notably, four DNA methyltransferases were identified and validated to play important role during browning in A. bisporus. Altogether, this study provides theoretical insights into the functions of DNMTs in A. bisporus, and offers new perspectives on the role of DNA methylation in edible mushrooms.