New Publication - Extensive intragenomic variation in the internal transcribed spacer region of fungi

In a recent publication, HUH Research Fellow Michael Bradshaw and colleagues evaluated multiple copies of the ITS region (the universal barcode for fungi) in over 2,000 different fungal species. Data revealed extensive intragenomic variation which can have wide implications for taxonomic and eDNA studies. The Open Access paper, "Extensive intragenomic variation in the internal transcribed spacer region of fungi," was published in iScience online July 10, 2023.

Summary: 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.

Michael J. Bradshaw, M. Catherine Aime, Antonis Rokas, Autumn Maust, Swarnalatha Moparthi, Keila Jellings, Alexander M. Pane, Dylan Hendricks, Binod Pandey, Yuanning Li, Donald H. Pfister. Extensive intragenomic variation in the internal transcribed spacer region of fungi. iScience, Volume 26, Issue 8, 2023. https://doi.org/10.1016/j.isci.2023.107317