Multiomic Analysis Provided Insights into the Responses of Carbon Sources by Wood-Rotting Fungi Daldinia carpinicola

<i>Daldinia carpinicola</i> is a newly identified species of wood-rotting fungi, with substantial aspects of its biology and ecological function yet to be clarified. A Nanopore third-generation sequencer was employed for de novo genome assembly to examine the genetic characteristics. The genome consisted of 35.93 Mb in 46 contigs with a scaffold N50 of 4.384 Mb. Glycoside hydrolases and activities enzymes accounted for a large proportion of the 522 identified carbohydrate-active enzymes (CAZymes), suggesting a strong wood degradation ability. Phylogenetic and comparative analysis revealed a close evolutionary relationship between <i>D. carpinicola</i> and <i>D. bambusicola</i>. <i>D. carpinicola</i> and <i>Hypoxylon fragiforme</i> exhibited significant collinear inter-species genome alignment. Based on transcriptome and metabolomic analyses, <i>D. carpinicola</i> showed a greater ability to utilize sucrose over sawdust as a carbon source, enhancing its growth by activating glycolysis/gluconeogenesis and the citrate cycle. However, compared with sucrose, sawdust as a carbon source activated <i>D. carpinicola</i> amino acid biosynthesis and the production of various secondary metabolites, including diterpenoid, indole alkaloid, folate, porphyrin, and biotin metabolism. The study establishes a theoretical basis for research and applications in biological processes, demonstrating a strategy to modulate the production of secondary metabolites by altering its carbon sources in <i>D. carpinicola</i>.