Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi

Fungi are among the most biodiverse organisms in the world. Accurate
species identification is imperative for studies on fungal ecology and
evolution. The internal transcribed spacer (ITS) rDNA region has been
widely accepted as the universal barcode for fungi. However, several
recent studies have uncovered intragenomic sequence variation within the
ITS in multiple fungal species. Here, we mined the genome of 2414 fungal
species to determine the prevalence of intragenomic variation and found
that the genomes of 641 species, about one-quarter of the 2414 species
examined, contained multiple ITS copies. Of those 641 species, 419 (~65%)
contained variation among copies revealing that intragenomic variation is
common in fungi. We proceeded to show how these copies could result in the
erroneous description of hundreds of fungal species and skew studies
evaluating eDNA especially when making diversity estimates. Additionally,
many genomes were found to be contaminated, especially those of
unculturable fungi.