Comparative genomics of the peach rot fungus Didymosphaeria rubi-ulmifolii reveal carbohydrate-active enzyme expansion and unique wood-decay strategies.

Didymosphaeriaceae is recognized for inducing canker and wood decay in fruit trees, but those genetic mechanisms underlying these processes remain largely unexplored. Here, our study investigates wood decay mechanisms in Didymosphaeria rubi-ulmifolii GF1, a strain associated with internal vascular discoloration and stem cankers in peach trees, by the combination of genome, transcriptome sequencing and gene silencing. The fungal genome assembly measured 40.4 Mb with 15,112 protein-coding genes, including 791 carbohydrate-active enzymes (CAZymes), revealing an expanded repertoire crucial for fungal metabolism. Transcriptome analysis of plant cell wall degrading enzymes uncovered the fungal functional adaptations to wood decay and pathogenicity. Furthermore, targeted gene silencing experiments using external dsRNA uptake effectively suppressed the expression of three lignin peroxidase genes and one manganese peroxidase gene, correlating with diminished fungal growth characteristics on peach tree wood, confirmed that those enzymes are involved in the lignin degradation for wood decaying. This comprehensive investigation provides novel insights into the wood decay mechanisms employed by plant pathogens, laying the groundwork for future studies aimed at effective management of plant diseases.