Characterization of lignocellulose degradation by Sparassis latifolia based on transcriptomics and weighted gene co-expression network analysis

Abstract:

[Objective] To explore gene expression profiles of Sparassis latifolia cultivated with different lignocellulose materials and provide a reference for mining the key genes and deciphering the mechanism of lignocellulose degradation by S. latifolia. [Methods] We examined the transcriptomes of S. latifolia cultivated in the liquid medium with pine, spruce, bagasse, fermented spruce, or fermented bagasse as the sole carbon source. Weighted gene co-expression network analysis (WGCNA) was performed on the gene expression of samples cultivated with different lignocellulose materials. [Results] There were only 20 differentially expressed genes (DEGs) between the spruce and pine groups, and 486 DEGs (the highest number) between bagasse and pine groups. Gene ontology (GO) enrichment analysis showed that the DEGs were mainly involved in oxidoreductase activity, monooxygenase activity, and iron ion binding. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed that the DEGs were mainly involved in pentose and glucuronate interconversions, methane metabolism, and glyoxylate and dicarboxylate metabolism. The expression of genes encoding glycoside hydrolases associated with cellulose or hemicellulose degradation was generally higher when the strain was cultured with fermented bagasse as the sole carbon source. The expression of genes encoding carbohydrate-active enzymes for lignin degradation or modification was generally higher when the strain was cultured with pine, spruce, or bagasse as the sole carbon source. A total of 10 co-expression modules were identified by WGCNA. Significant positive correlations existed between the green module and bagasse, between the blue module and fermented bagasse, and between magenta and turquoise modules and fermented spruce. GO enrichment analysis showed that the genes in the turquoise module were enriched in urea transmembrane transporter activity, methyltransferase activity, and monooxygenase activity, while those in the blue module in hydrolase activity and β-mannosidase activity. KEGG pathway enrichment analysis showed that the genes in the blue module were enriched in galactose metabolism, fructose and mannose metabolism, phenylalanine metabolism, arginine and proline metabolism, etc. From the interaction network, 12 hub genes were obtained, which may be involved in lignocellulose degradation or gene expression regulation. [Conclusion] Different lignocellulose materials significantly affected the gene expression profiles ofS. latifolia, which may imply the specific degradation strategies against different lignocellulose materials.