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Background Drought stress severely restricts edible fungus production. The genus  Auricularia  has a rare drought tolerance, a rehydration capability, and is nutrient rich. Results The key genes and metabolic pathways involved in drought-stress and rehydration were investigated using a transcriptome analysis to clarify the relevant molecular mechanisms. In total, 173.93 Mb clean reads, 26.09 Gb of data bulk, and 52,954 unigenes were obtained. Under drought-stress and rehydration conditions, 14,235 and 8539 differentially expressed genes, respectively, were detected. ‘Tyrosine metabolic’, ‘caffeine metabolism’, ‘ribosome’, ‘phagosome’, and ‘proline and arginine metabolism’, as well as ‘peroxisome’ and ‘mitogen-activated protein kinase signaling’ pathways, had major roles in  A. fibrillifera  responses to drought stress. ‘Tyrosine’ and ‘caffeine metabolism’ might reveal unknown mechanisms for the antioxidation of  A. fibrillifera  under drought-stress conditions. During the rehydration process, ‘diterpenoid biosynthesis’, ‘butanoate metabolism’, ‘C 5 -branched dibasic acid’, and ‘aflatoxin biosynthesis’ pathways were significantly enriched. Gibberellins and γ-aminobutyric acid were important in the recovery of  A. fibrillifera  growth after rehydration. Many genes related to antibiotics, vitamins, and other health-related ingredients were found in  A. fibrillifera . Conclusion These findings suggested that the candidate genes and metabolites involved in crucial biological pathways might regulate the drought tolerance or rehydration of  Auricularia , shedding light on the corresponding mechanisms and providing new potential targets for the breeding and cultivation of drought-tolerant fungi.

Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration