Genomic and Proteomic Analysis of Functional Genes in Phacidium infestans DSM 5139 for Nutrient Acquisition and Ecosystem Functioning

Phacidium infestans Karsten DSM 5139 is a significant fungal pathogen that causes snow blight in conifers across Europe and Asia. Thriving under snow cover, P. infestans infects and kills pine needles, which are known for their antifungal properties. The genome of the strain DSM 5139 was sequenced using PacBio II technology, resulting in 44 contigs with a genome size of ~36.8 Mb and a GC content of 46.4%. Genome completeness was assessed at 98.6% using BUSCO analysis, and its annotation revealed 11,357 open reading frames. Functional annotation identified 573 carbohydrate-active enzymes and approximately 400 genes linked to secondary metabolite biosynthesis.

Several mechanisms facilitating P. infestans survival and proliferation on pine needles were identified, including drug-efflux pumps, acyclic terpene synthases, and phytoalexin detoxification enzymes. Two cutinase proteins were detected. Their protein modeling confirmed the presence of functional structures such as signal peptides, catalytic triads, and lid domains. In addition, numerous cold-survival strategies were identified including trehalose synthesis enzymes, desaturases, stress response proteins, and two ice-binding proteins that modulate ice crystal formation at subzero temperatures.

Pathway reconstruction revealed an efficient nutrient acquisition strategy.  First, the fungus breaches the needle waxes using secreted cutinases. Then it degrades the plant cell wall polymers with cellulases, pectinases, lignin-degrading enzymes, and other plant cell wall-degrading enzymes.

This study represents one of the first comprehensive genomic analyses of P. infestans, providing valuable insights into its genomic adaptations for nutrient acquisition and survival in cold environments. The findings enhance our understanding of fungal-plant interactions and highlight the ecosystem functioning of this fungal pathogen in forest ecosystems.