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Background: Flammulina filiformis (=Asian “F.velutipes”) is a popular commercial edible mushroom. Many bioactive compounds such as polysaccharides and sesquiterpenoids with medicinal effects have been isolated and identified, but their biosynthesis and regulation in molecular level is unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu 355, predicated the biosynthetic gene clusters (BGCs) and profiled these genes expression between wild and cultivar strains and among different development stages of the wild strain of F. filiformis by a comparative transcriptomic analysis. Results: The results revealed that the genome of the F. filiformis was 35.01 M bp in length and annotated with 10396 gene models. 12 putative terpeniod gene clusters were predicted, 12 sesquiterpenes synthase genes belonged to four different groups and two type I PKS (polyketide synthase) gene clusters were identified from F. filiformis genome. The gene number related terpeniod biosynthesis is higher in wild strain (119 genes) than cultivar strain (81 genes) and most of them are up regulated in primodium and fruiting body of the wild strain, while PKS genes are usually up-regulated in the mycelium of wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase involved in polysaccharide biosynthesis have relative high transcripts both in mycelium and fruiting bodies of F. filiformis. Conclusions: We identified candidate genes involved in the biosynthesis of polysaccharide and terpenoid bioactive compounds and profiled these genes expression during the development of F. filiformis. This study expends our knowledge for understanding the biology of F. filiformis and provides valuable data for elucidating the secondary metabolism regulation of the special strain of F. filiformis.

Background: Flammulina filiformis (=Asian “F.velutipes”) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicated its the biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wild F. filiformis strain by a comparative transcriptomic analysis. Results: We found that the genome of the F. filiformis was 35.01 M bp in length and harbored 10396 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 the F. filiformis genome. 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 wild F. filiformis strain. Conclusions: F. filiformis is 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 of F. filiformis and provides valuable data for elucidating the regulation of secondary metabolites in this unique F. filiformis strain.