Secondary structure of the ITS2 region of the ribosomal DNA of micromycetes section Sclerotiorum as an additional phylogenetic marker

DOI: https://doi.org/10.7124/FEEO.v36.1726
Keywords: Sclerotiorum, Adamentziorum, ribosomal DNA, ITS2 region, secondary structure of DNA

Abstract

Aim. The phylogeny of microscopic fungi of the genus Penicillium of the section Sclerotiorum is still poorly understood. Therefore, the aim of the study was to build a consensus model of the secondary structure of the ITS2 rDNA region based on a representative species of P. bilaiae and closely related fungal species and to determine the possibility of its use as an additional phylogenetic marker. Methods. The methods used in the study were comparative analysis of primary DNA sequences, construction of their secondary structure based on the least free energy (MFE RNAfold) and analysis of conserved structures and mutation points. Results. The ITS2 region of the Sclerotiorum серії Adamentziorum section consists of 150–170 bp. The secondary structure according to MFE RNAfold forms three classical hairpins. The sequence of the second loop from the 5'-end of the structure was recognized as crucial for the identification of the studied species. Conclusions. The secondary structure of the ITS2 region of rDNA can be used as an additional marker for the molecular identification of P. bilaiae and closely related representatives of the section Sclerotiorum.

References

Wang X. C., Chen K., Zeng Z. Q., Zhuang W. Y. Phylogeny and morphological analyses of Penicillium section Sclerotiora (Fungi) lead to the discovery of five new species. Sci Rep. 2017. 7. P. 8233 https://doi.org/10.1038/s41598-017-08697-1.

Bengtsson-Palme J., Ryberg M., Hartmann M. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution. 2013. Vol. 4 (10). P. 914–919. https://doi.org/10.1111/2041-210X.12073.

Lücking R., Aime M. C., Robbertse B. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol. 2021. 6. P. 540–548. https://doi.org/10.1038/s41564-021-00888-x.

Yang R. H., Su J .H., Shang J. J. et al. Evaluation of the Ribosomal DNA Internal Transcribed Spacer (ITS), Specifically ITS1 and ITS2, for the Analysis of Fungal Diversity by Deep Sequencing. PLoS ONE. 2018. 13. e0206428. https://doi.org/10.1371/journal.pone.0206428.

Houbraken J., Kocsubé S., Visagie C. M. et al. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Studies in Mycology. 2020. Vol. 95 (1). P. 5–169. https://doi.org/10.1016/j.simyco.2020.05.002.

Ramos S. M. S., Cruz R., Barbosa R. d. N. et al. Two new Penicillium section Sclerotiorum species from sugarcane soil in Brazil. Mycol Progress. 2020. 20. P. 823–835. https://doi.org/10.1007/s11557-021-01705-9.

Pieczul K., Świerczyńska I., Wójtowicz A. Advanced rDNA-Based Detection of Wheat Pathogens in Grain Samples Using Next-Generation Sequencing (NGS). Pathogens. 2025. 14 (2). P. 164. https://doi.org/10.3390/pathogens14020164.