The Challenge

DNA barcoding of fungal species faces a number of challenges. Because the majority of fungi are microscopic, their presence is often not obvious. Their presence is often inferred indirectly, either by the isolation of cultures, or increasingly, by the detection of their DNA. Studies of so-called environmental DNA have recovered huge numbers of sequences that appear to represent unknown fungi; several large lineages have been discovered that do not correspond with sequences of known fungi groups.

Species concepts in fungi are inconsistently applied, and species recognized by classical methods (i.e by morphology) are usually more broadly delimited than those recognized by genetic (mating) studies or DNA-based molecular methods.

Fungal pleomorphy, the tendency for a single fungal genome to produce more than one morphological type of sporulation, complicates the taxonomy of large groups of fungi, especially the Ascomycetes and the rusts. In some fungi, the different sporulating forms receive different scientific names, making fungal taxonomy a puzzling world for the uninitiated.

The Opportunities

Mycology has a proud history of the application of DNA sequences to taxonomic and phylogenetic problems. Tens of thousands of fungal sequences derived from taxonomic studies are available in the public DNA sequence databases. Multi-gene phylogenies are now a routine aspect of most taxonomic revisions.

Standardization on a common barcode for identification is a topic that must now be addressed. The development of a verified ‘barcode’ subset of the existing data will enable us to pass over the unidentified environmental sequences and misidentified sequences.

Fungi are important sources of food, antibiotics, and medicines. Their negative economic impacts include biodeterioration, toxin production, contamination of indoor air, and diseases of animals and plants. The development of effective DNA barcode tools will be of great value.

The Future

The application of molecular methods to fungal biosystematics is expanding rapidly. DNA barcodes for species recognition will be complemented by more in-dept, multi-locus studies aimed at phylogenetic species recognition and the assessment of phylogenetic relationships. Eventually, such studies will be extended to include whole-genome, SNP-based haplotype mapping, and the development of DNA arrays for monitoring fungi and other microorganisms in the environment. As we travel down this exciting path of discovery in the fungal realm, the tagging of taxa with DNA barcodes will continue to facilitate the research taxonomists, evolutionary biologists, field ecologists and biodiversity managers.