Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation

Abstract

Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.

Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming FungusFlammulina velutipes

“…The genome sequence of strain KACC42780 (Park et al 2014) was provided by W.S. Kong of the Rural Development Administration (RDA) in Korea.…”

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

“…Genome sequence data have been published for basidiomycetous fungi such as Phanerochaete chrysosporium (8), Laccaria bicolor (9), Coprinopsis cinerea (10), Agaricus bisporus (11), Schizophyllum commune (12), and Flammulina velutipes (13). Because of the popularity of next-generation sequencing, many genome sequence drafts of basidiomycetous fungi are publicly available, especially from the 1,000 Fungal Genomes Project (14).…”

The multigene family of fungal laccases and their expression in the white rot basidiomycete Flammulina velutipes

“…In addition, a laccase gene fvlac7, was cloned based on the genomic sequence of F. velutipes and heterologously over-expressed in an Escherichia coli system (Kim et al, 2013). Because of its high nutritional and medicinal value and scale of production, F. velutipes has been recognized as a useful model fungal species to study matrix degradation in edible mushrooms (Park et al, 2014).…”