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

Area of Science:

• Mycology and Molecular Systematics
• Fungal Genomics and Bioinformatics

Background:

• Mushrooms are vital fungi, but their classification is difficult due to shared traits and hidden diversity.
• Traditional methods struggle with accurate mushroom identification and evolutionary studies.

Purpose of the Study:

• To review advancements in molecular techniques for mushroom systematics.
• To highlight the integration of DNA barcoding, phylogenomics, and multi-omics.

Main Methods:

• Utilizing DNA barcoding, particularly the internal transcribed spacer (ITS) region.
• Employing multilocus and genome-scale datasets for phylogenomic analysis.
• Integrating multi-omics platforms (genomics, transcriptomics, proteomics, metabolomics).

Main Results:

• Phylogenomic and multi-omics approaches refine species boundaries and evolutionary understanding.
• High-throughput sequencing and whole-genome data enhance resolution of fungal lineages.
• Omics data offer holistic insights into fungal functions and adaptations.

Conclusions:

• Molecular systematics, especially phylogenomics and omics, are transforming fungal classification.
• Standardization, AI, and open data are crucial for future progress in fungal systematics.
• An integrative, data-driven framework is essential for understanding and utilizing fungal diversity.