Background: Fungal biotechnology contributes significantly to global enzyme production and industrial fermentation. Due to the complexity of fungal genomes, combined with their multi-omics and intricate biological systems, computational approaches exhibit growing importance for understanding genomic variation and functional diversity. Pangenome graphs provide a comparative, multi-taxon methodology that has proven effective in characterizing fungal pathogenicity to plants and identifying accessory genes. Their applications to fungal strain design and biotechnological innovations remain underexplored. In addition, constructing high-quality pangenome graphs is computationally demanding, which limits broader adoption. In contrast, fungal genome annotation tools offer rapid annotations for newly sequenced isolates and can serve as complementary resources for enhancing pangenome analyses. In this study, we propose an integrative framework that combines pangenome graph construction, genome annotation, and downstream analytical methods. This framework aims to enhance the interpretability of fungal genomic variation and support future advances in gene function prediction.