Risk assessments of the degeneration in Flammulina filiformis based on the transcriptome analysis

The mushroom Flammulina filiformis is an important food supplement. In large-scale production, strain degeneration occurs frequently and affects the quality and productivity of the product and thus causes serious economic loss. The regulative mechanism underlying strain degeneration remains unclear and an effective method to discriminate degenerate strain is urgently needed. In this study, two F. filiformis strains, a normal strain named F1 and its sixth generation of successive culture named F7 were used to construct a transcriptome assembly. Compared to F1, F7 exhibited similar vegetative growth but potentially degenerated. A total of 12,385 unigenes of F1 and F7 were assembled. Functions of these unigenes were annotated based on the Blast results against databases such as NCBI non-redundant protein sequences, eggNOG and Swissprot databases. A total of 632 different expressed genes (DEGs) in F17 were identified with down- or up-regulation compared those in F11. Among these DEGs, 352 were down-regulated and 280 were up-regulated. GO enrichment analysis of DEGs indicated that the classification oxidoreductase activity was highly enriched, having the most numbers of DEGs compared to other categories. KEGG pathway enrichment analysis indicated the peroxisome pathway was highly enriched. Based on the RNA-seq analysis, an assay for stress tolerance of F. filiformis was developed by culturing strain in media supplemented with H2O2, SDS, congo red or NaCl. This assay can be used to evaluate the risk of strain degeneration and discriminate the degenerated strains. The fruiting body production was use to validate the risk assessment results. Our data suggest that degeneration of F. filiformis is associated with oxidoreductase stress and could be predicted by the developed assay, which provides a useful method for F. filiformis producers to predict strain degeneration in commercial mushroom production.