DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.

Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.