# 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.

## Key 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.