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.
Highlights
Flammulina elastica (Physalgacriaceae; white-rotting basidiomycete) was first recognized in 1999 by Redhead and Petersen [1]; little is known about its biology, including its molecular characteristics
F. velutipes was found to convert cellobiose, cellotetraose, cellotriose, maltose, and sucrose to ethanol, with similar recovery rates as that of glucose. These capabilities of F. velutipes can be applied to bioethanol production processing, which is known as consolidated bioprocessing (CBP)
CBP is considered an effective alternative to high-cost biomass processing for bioethanol production from lignocellulosic biomass [90,91,92]
Summary
Flammulina elastica (Physalgacriaceae; white-rotting basidiomycete) was first recognized in 1999 by Redhead and Petersen [1]; little is known about its biology, including its molecular characteristics. F. elastica spores were reported to differ from those of Flammulina velutipes with SQ = 2.5–3 (the ratio of length and width of the spores) [2]. Ripková et al [3] reported that F. elastica had similar morphological characteristics to F. velutipes, but some specimens identified morphologically as F. velutipes had F. elastica internal transcribed spacer (ITS) sequences. F. elastica was found to be basal to F. velutipes based on a phylogenetic analysis of ITS DNA sequences. These discoveries indicated that further investigations were needed to resolve these discrepancies for morphological and molecular delimitation. F. elastica is generally considered lignicolous, with direct growth from wood [4]
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