Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis

Abstract

Background Flammulina filiformis (previously known as 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, 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 wild F. filiformis strain by a comparative transcriptomic analysis. Results We found that the genome of the F. filiformis was 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 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.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

“…(Chen et al 2012), Flammulina spp. (Park et al 2014(Park et al , 2019Chen et al 2020), L. edodes (Berk.) Pegler (Chen et al 2016;Shim et al 2016;Sakamoto et al 2017a), Pleurotus spp (A et al 2018;Wang et al 2018a;Dai et al 2019;Lee et al 2021), Agaricus spp (Morin et al 2012;O'Connor et al 2019;Sonnenberg et al 2020), Tricholoma matsutake (S. Ito & S. Imai) Singer (Min et al 2020), Sparassis crispa (Wulfen) Fr.…”

Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu)

“…In a follow-up study, Yan et al optimized the protoplast preparation method of S. rugosoannulata, which is useful in crossbreeding or transformation [25]. However, compared with other mushrooms, such as Auricularia, Lentinuta, Agaricus, Coprinopsis, and Fillumina [26][27][28][29][30][31][32][33][34], there are few biological and genetic studies on S. rugosoannulata, which impedes the breeding of high-quality cultivars. The lack of genomic information is one of the main reasons limiting the further study of this mushroom.…”

Comprehensive Genetic Analysis of Monokaryon and Dikaryon Populations Provides Insight Into Cross-Breeding of Flammulina filiformis

“…F. filiformis from eastern Asia differs from the European F. velutipes according to recent phylogenetic results based on multi-gene markers and morphological comparisons ( Wang et al, 2018 ). F. filiformis is a widely cultivated and consumed edible fungus with high dietary and medicinal value ( Rahman et al, 2015 ; Tang et al, 2016 ; Chen et al, 2020 ). It is also one of the most professional and productive edible fungi in industrialized cultivation ( Bao et al, 2009 ).…”