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

TL;DR

This study explores how the wood-rotting fungus Daldinia carpinicola uses different carbon sources, revealing insights into its genome and metabolism.

Contribution

The study provides new insights into the genomic and metabolic responses of Daldinia carpinicola to different carbon sources.

Findings

Daldinia carpinicola has a genome with strong wood degradation potential due to a high proportion of glycoside hydrolases and CAZymes.

Transcriptome and metabolomic analyses show D. carpinicola prefers sucrose over sawdust for growth, activating glycolysis and the citrate cycle.

Sawdust as a carbon source enhances amino acid biosynthesis and production of secondary metabolites in D. carpinicola.

Abstract

Daldinia carpinicola 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 D. carpinicola and D. bambusicola. D. carpinicola and Hypoxylon fragiforme exhibited significant collinear inter-species genome alignment. Based on transcriptome and metabolomic analyses, D. carpinicola 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 D. carpinicola 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 D. carpinicola.

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