Genome-Wide Analysis And Prediction Of Genes Involved In The Biosynthesis Of Polysaccharides And Bioactive Secondary Metabolites In High-Temperature-Tolerant Wildflammulina Filiformis

Background Flammulina filiformis(previously known as AsianF. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified fromF. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strainF. filiformisLiu355, predicted its biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wildF. filiformisstrain by a comparative transcriptomic analysis. Results We found that the genome of theF. filiformiswas 35.01 Mb in length and harbored 10,396 gene models. Thirteen putative terpenoid gene clusters were predicted and 12 sesquiterpene synthase genes belonging to four different groups and two type I polyketide synthase gene clusters were identified in theF. filiformisgenome. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Most terpenoid biosynthesis genes were upregulated in the primordium and fruiting body of the wild strain, while the polyketide synthase genes were generally upregulated in the mycelium of the wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase, which are involved in polysaccharide biosynthesis, had relatively high transcript levels both in the mycelium and fruiting body of the wildF. filiformisstrain. Conclusions F. filiformisis enriched in a number of gene clusters involved in the biosynthesis of polysaccharides and terpenoid bioactive compounds and these genes usually display differential expression between wild and cultivar strains, even in different developmental stages. This study expands our knowledge of the biology ofF. filiformisand provides valuable data for elucidating the regulation of secondary metabolites in this uniqueF. filiformisstrain.