Flammulina Genome sequencing and assembly. Flammulina

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. 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. This study expends our knowledge for biology of F. filiformis and provides valuable clues for identifying candidate genes involved in the biosynthesis of polysaccharide and terpenoid bioactive compounds.