Transcriptomics analysis and co-expression network revealing candidate genes for laccase activity of Lenzites gibbosa

Abstract Background Lenzites gibbosa is a common white-rot fungus of Polyporaceae in the cold temperate zone which cause spongy white decay of wood. Results In this study, the lignin degradation pathway of L. gibbosa at 5-time points under wood treatment was studied by RNA-Req technology. A total of 5232 DEGs were identified from 15 libraries. In 0–3 days, the mycelia are in the adaptive stage, and the mycelia began to proliferate within 3–5 days. After 5 days, the number of DGEs decreased significantly, the mycelium growth entered the platform stage, and the life activity was basically stable. In the secondary metabolism, oxidoreductase such as laccase, 2-oxoglutarate-Fe (II) type oxidoreductase, peroxisomal hydratase-dehydrogenase, dual-functional monooxygenase dominated and increased steadily, and manganese peroxidase appeared in the middle stage. With the accumulation of lignin intermediate products, P450 and ABC transporters were from the inhibition to the activation. Weighted gene co-expression network analysis (WGCNA) showed that among the 24 modules 6 modules were significantly correlated with laccase activity and the most correlated were turquoise and blue module. The central hub genes were also identified, including gene_7458, gene_61, gene_7458, gene_1741, gene_11087 which were consistent with the DGEs. These genes have high connectivity, module membership, and gene significance in the module. The enrichment analysis of GO and KEGG pathway indicated that the genes involved in cell cycle, citrate cycle (TCA cycle), nicotinate and nicotinamide metabolism, mitochondrial outer membrane, succinate dehydrogenase, carboxypeptidase and exopeptidase activity, flavin adenine dinucleotide binding, oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor pathway were highly related to laccase synthesis pathway. Construction of gene co-expression network and hypothetical L. gibbosa laccase synthesis pathway. Conclusion This study focused on the screening of L. gibbosa degradation of lignin-related genes. And, this is the first study reporting co-expression patterns of a gene network in L. gibbosa laccase activity after wood treatment which is helpful to understand the synthesis pathway of laccase and improve the activity of laccase, which can be used to increase the rate of lignin degradation by L. gibbosa in the further.