Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Abstract

Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

Metagenomic Insights Into the Taxonomic and Functional Features of Kinema, a Traditional Fermented Soybean Product of Sikkim Himalaya

“…Kinema metagenome displayed the diverse set of CAZYmes that could be interactive with the carbohydrate, which constitutes 35% of soybean seeds (Karr-Lilienthal et al, 2005; Hou et al, 2009). The GH and GT family enzymes, which could be belonging to the phylum Firmicutes and Proteobacteria, respectively, perform an interplay in the processing of carbohydrate macromolecules during fermentation (Park et al, 2018). This results in the biosynthesis of disaccharide, oligosaccharide, and glycoconjugates (Van Laere et al, 2000; Breton et al, 2006).…”

Genomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae

“…This feature may readily be inferred from the current comparison, where on the average the free-living fungi of the genera Apiotrichum and Vanrija harbour greater numbers of CAZYmes than the predominantly host-associated Trichosporon and Cutaneotrichosporon taxa. Furthermore, the abundance of GHs and CEs 28 in Apiotrichum and Vanrija, respectively may reflect their capacity to breakdown and utilise wide range of www.nature.com/scientificreports www.nature.com/scientificreports/ substrates. These taxa are frequently isolated from soil and other environments where they degrade and subsist on various forms of complex substrates 29 .…”

Genomic-wide analysis and prediction of genes involved in biosynthesis of polysaccharide and bioactive secondary metabolites in high-temperature-tolerance of wild Flammulina filiformis

“…Development of "omic" technology provided the powerful tools to understand the biology of edible mushroom including effective utilization for cultivation substrate (lignocellulose) [28,29], the mechanism of fruiting body's formation and development and adaption for environment such as high temperature or cold stress [30,31,32]. For example, genome sequencing of the cultivars of F.velutipes from Korea and Japan revealed the high capacity for lignocellulose degradation [28,33].…”