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. 2018 Nov 16;46(4):349-360.
doi: 10.1080/12298093.2018.1537585. eCollection 2018.

Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis

Young-Jin Park  1 , Won-Sik Kong  2
Affiliations

Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis

Young-Jin Park et al. Mycobiology. .

Abstract

Whole-genome sequencing of Flammulina ononidis, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of de novo genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one F. ononidis gene. In addition, 11,252 (89.5%) of 12,586 genes for F. ononidis proteins had orthologs among the Dikarya, and F. ononidis contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the F. ononidis genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus F. ononidis.

Keywords: Flammulina ononidis; carbohydrate-active enzyme; genome.

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Figures

Figure 1.
Figure 1.
Phylogenetic tree of fungal species based on ortholog clustering. The amino acid sequences in each orthologous group were aligned by MAFFT (https://mafft.cbrc.jp/alignment/software/) and phylogenetic tree was constructed with FastTree (http://www.microbesonline.org/fasttree/) with 1000 bootstraps.
Figure 2.
Figure 2.
CAZyme distribution predicted from F. ononidis genome. The number after each CAZyme means family. (a) GT families; (b) GH families; (c) AA, CBM, CE, and PL families. AA, auxiliary activities; GH, glycoside hydrolase; GT, glycosyltransferase; CBM, carbohydrates- binding module; PL, polysaccharide lyase.
Figure 3.
Figure 3.
Venn diagrams of CAZymes predicted in F. ononidis by three different database searches including protein family database (Pfam), CAZyme database (dbCAN), and National Center for Biotechnology Information (NCBI) non-redundant database (NCBI-NR). (a) GT families; (b) GH families; (c) PL families; (d) CBM families; (e) CE families; and (f) AA families.
Figure 4.
Figure 4.
Conserved motifs within (a) glycoside hydrolase family 16, (b) carbohydrate esterase family 1, (c) carbohydrate esterase family 16, (d) auxiliary activity family 1 (laccase), and (e) auxiliary activity family 3 (GMC oxidoreductase) amino acids of F. ononidis. Position (a.a.) refers to the start and end positions of the motif in the amino acid sequence.
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