Domains of Life: Fungi
It has been estimated that global fungal diversity totals 1.5 million species, but less than ten percent of these have been formally described (Kirk et al. 2001). Fungi are of considerable economic importance, not only because of their well known role in many fermentation processes, but also as causative agents of plant and animal diseases, as allergens, as sources of antibiotic production, and increasingly for their use in bio-control. Fungi also feature prominently in the list of invasive alien species in Canada, with prominent examples including the pathogens causing white pine blister rust, potato wart, soybean rust, and most recently, Sudden Oak Death. The deployment of DNA barcoding for the efficient detection and identification of both pathogenic and beneficial fungi will be crucial for protecting and enhancing the health of our forests and crops.
The creation of stable taxonomic systems has proven difficult for many fungal groups because of the limited number of distinctive morphological characters exhibited by these organisms. Not only have higher-level taxa been shown to be heterogeneous, but even basic species concepts are commonly called into question by new molecular data (see Taylor et al.2000). In the present context, we use the colloquial term “fungi” to include members of what are now recognized as two distinct kingdoms: the Mycota and Straminipila (Money 1998). Past taxonomic efforts have been directed largely towards Basidiomycetes and Ascomycetes that sporadically produce conspicuous fruiting bodies, but spend most of their life as sterile, microscopic hyphae. However, it is obvious that a system is needed that is capable of identifying all fungi, be they macroscopic or microscopic, and regardless of life stage. This is especially true in practical situations such as the study of asymptomatic material (Hamelin et al. 2000).
Already, there is a large ribosomal DNA (rDNA) database for fungi, representing about 12% of described species, based on sequences from the nuclear large subunit RNA (LSU) gene and the internal transcribed spacer (ITS). These rDNA sequences, particularly ITS, have been successfully exploited as species markers in some fungal groups (e.g. Basidiomycetes and Oomycetes), but these sequences are too conserved in some Ascomycetes and related moulds. In these cases, identifications can currently only be done at taxonomic ranks above the species level. The US-NSF Assembling the Tree of Life Program has funded the development of a comprehensive phylogeny of the Fungi based on 7 genes (but not including COI) of 1,000-2,000 species. However, that program does not consider species level identifications and, consequently, is complementary to our objectives to develop species diagnostics for selected groups.
One potential complication for DNA barcoding of fungal species is the fact that, unlike animals, the mitochondrial genes of fungi are frequently interrupted by introns. One solution to this problem would be to focus on the characterization of sequences obtained from cDNA libraries from which introns have already been spliced, an approach that has shown promise in rusts (Joly et al. 2003). Alternatively, it may be useful to employ RT-PCR methods to amplify mRNA sequences rather than genomic DNA. These methodological challenges aside, the presence of introns does provide some advantages, for example by facilitating the resolution of closely related taxa by virtue of their accelerated rates of sequence divergence. This also makes it possible to carry out surveys of the distribution of mobile mitochondrial introns in natural populations.