Extensive intragenomic variation in the internal transcribed spacer 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 environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.

Automated summary

Fungi are highly biodiverse organisms and accurate species identification is crucial for ecological and evolutionary studies. The internal transcribed spacer (ITS) rDNA region is commonly used as a barcode for fungi, but recent studies have found intragenomic sequence variation within ITS in many fungal species. Genome mining of 2414 fungal species revealed that about 25% of them had multiple copies of ITS, and among these species, 65% showed variation among the copies. This intragenomic variation can lead to inaccurate descriptions and bias in studies evaluating environmental DNA (eDNA).