Abstract
More than a decade ago a short tandem repeat-based typing method was developed for the fungus Aspergillus fumigatus. This STRAf assay is based on the analysis of nine short tandem repeat markers. Interpretation of this STRAf assay is complicated when there are only one or two differences in tandem repeat markers between isolates, as the stability of these markers is unknown. To determine the stability of these nine markers, a STRAf assay was performed on 73–100 successive generations of five clonally expanded A. fumigatus isolates. In a total of 473 generations we found five times an increase of one tandem repeat unit. Three changes were found in the trinucleotide repeat marker STRAf 3A, while the other two were found in the trinucleotide repeat marker STRAf 3C. The di- or tetranucleotide repeats were not altered. The altered STRAf markers 3A and 3C demonstrated the highest number of repeat units (≥50) as compared to the other markers (≤26). Altogether, we demonstrated that 7 of 9 STRAf markers remain stable for 473 generations and that the frequency of alterations in tandem repeats is positively correlated with the number of repeats. The potential low level instability of STRAf markers 3A and 3C should be taken into account when interpreting STRAf data during an outbreak.
Highlights
Tandem repeats are repetitive DNA sequences of 1 or more nucleotides, which are abundantly present in eukaryotic genomes, both in coding and non-coding regions (Gemayel et al, 2010)
More than 10 years ago a short tandem repeats (STRs)-based analysis to type A. fumigatus (STRAf ) was developed that consists of three times three di, tri, or tetra-nucleotides repeat markers
Information regarding the stability of the STR markers of A. fumigatus was rather limited
Summary
Tandem repeats are repetitive DNA sequences of 1 or more nucleotides, which are abundantly present in eukaryotic genomes, both in coding and non-coding regions (Gemayel et al, 2010). They are characterized by their highly polymorphic nature, as the number of repeated sequences often varies within species (Genovese et al, 2018). This polymorphic nature plays an important role in adaptation toward environmental changes by affecting cellular processes like cell surface variability, plasticity in body morphology and tuning of the circadian rhythm.
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