2012: ITS becomes the fungal barcode

In 2012 the Fungal Barcoding Consortium published in the Proceedings of the National Academy of Sciences a comparison of six DNA regions used to identify fungi. The aim was not to find a marker ideal for every genus, but to select a common point of reference that can be amplified effectively across very different lineages. The internal transcribed spacer of ribosomal DNA — ITS — was adopted as the kingdom's primary barcode.

The team compared ribosomal fragments with regions of protein-coding genes. Some protein genes separated species better within particular groups, but far more often failed at the stage of obtaining a PCR product and a sequence. ITS offered the best compromise between the universality of primers, the quantity of available data and the power to discriminate. The decision therefore followed from a multi-criteria test, not from a conviction that a single fragment would solve every taxonomic puzzle.

The publication harmonised the work of laboratories, collections and environmental databases. A sequence from a fruiting body, a culture or a sample could be compared with an ever-growing reference library. This accelerated the detection of hidden diversity, the checking of identifications, and studies of communities without culturing every organism. At the same time it exposed the problem of misnamed sequences and of gaps for types and rare species.

ITS does not always separate closely related species, and in some groups there is variation within a single genome. A good similarity score does not replace sample quality, a phylogenetic tree, morphology and ecology. The historical significance of 2012 lies in establishing a shared infrastructure for comparison. A barcode is a working standard, not an automatic verdict on a name.

Not the most resolving marker, but the most universal

The 2012 consortium compared six DNA regions: three parts of the nuclear ribosomal cistron (SSU, ITS and LSU) and three protein-coding genes (RPB1, RPB2 and MCM7). Sampling covered representatives of 17 major fungal lineages. Protein-coding regions often separated species more successfully, but their much lower PCR and sequencing success ruled them out as a single kingdom-wide marker. ITS produced an overall probability of correct identification of 0.73; the value was 0.79 for the major macrofungal groups of Basidiomycota and 0.75 for filamentous Ascomycota. LSU performed better in some early-diverging lineages and in ascomycete yeasts.