Combining transcriptomics and metabolomics to characterize ergosterol biosynthesis in Flammulina velutipes during the fruiting process

Abstract

Background: Flammulina velutipes (F. velutipes) is one of the most important mushrooms in Japan and China because of its potential medicinal and nutritional value. Ergosterol is an important precursor of vitamin D2, progesterone, hydrocortisone, brassinolide, and novel anticancer and anti-HIV drugs. One of the main methods for obtaining ergosterol is extraction of its natural products from fungi. However, because of the low production of ergosterol due to its inefficient biosynthesis, its approach cannot meet human needs. Therefore, increasing the ergosterol level in fungi is an important goal to be pursued. Although genes encoding key enzymes in the biosynthesis pathway of ergosterol have been identified in Saccharomyces cerevisiae, the mechanism and regulation of ergosterol biosynthesis in F. velutipes remain unclear, and are the focus of this study. Results: In this work, nine cDNA libraries produced from the three stages of F. velutipes were sequenced by using the Illumina HiSeqTM 4000 platform, resulting in at least 6.63 Gb of clean reads from each library. De novo sequence assemblers were used to generate 220,523 transcripts and 28,330 unigenes, which were annotated according to seven protein databases. Here, we combined transcriptomics and metabolomics approaches to investigate the biosynthesis of bioactive ergosterol from F. velutipes. The contents of 16 intermediates or metabolites from different stages (young fruiting body stage and mycelium stage) were found to be significantly different. Then, transcriptional profiling of the genes involved in ergosterol biosynthesis was carried out, and the transcripts of key genes involved in the metabolism were analysed. A total of 51 key unigenes (12 upregulated unigenes and 39 downregulated unigenes) were identified as differentially expressed. Furthermore, four genes (i.e., ERG10s, ERG1s, ERG11s and ERG26s) were identified as the most important genes that played roles in the regulation of the pathway flux towards ergosterol synthesis in F. velutipes. Combining transcriptomics and metabolomics, we explored the regulatory relationship between ergosterol biosynthesis genes and metabolites in F. velutipes. Conclusions: The data obtained in this work provide useful information for understanding the biosynthesis, metabolism and regulation of sterols in F. velutipes and for channelling the metabolic flux towards ergosterol at different growth stages.