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bioRxiv · 10.1101/2025.11.13.688250

Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae

Dudragne, L.·Bernardes, J. S.·Xu, Z.
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Abstract

The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y elements represent a major class of subtelomeric repeats, yet their diversity and evolutionary dynamics remain incompletely characterized. Here, we analyzed Y elements across 54 S. cerevisiae strains using high-quality telomere-to-telomere genome assemblies. We detected 893 high-confidence Y elements, which we classified into 12 major clusters, revealing a broader structural diversity than previously described, including canonical short ([~]5.2 kb) and long ([~]6.7 kb) elements, intermediate-size classes (mid1 and mid2), and a novel family containing CA-rich repeats. Sequence analyses showed that open reading frames (ORFs), including those encoding the putative Y-Help1 helicase, are highly conserved within clusters, suggesting selective maintenance of functional sequences. The distribution of Y elements varied widely across strains and chromosome extremities, with some strains lacking Y entirely and others, such as the clinical ADI isolate, carrying up to 149 copies. Interstitial telomeric sequences (ITS) were variably associated with Y elements and tandem Y repeats, potentially facilitating recombination and amplification. Analysis of telomere length data further revealed that the presence of long Y' elements, but not Y elements from other clusters, at the subtelomere is correlated with shorter telomeres at the same chromosome end. Our results provide the most comprehensive catalog of S. cerevisiae Y elements to date, uncovering unexpected structural and sequence diversity, and a potentially functional role in telomere length regulation.

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Dudragne, L., Bernardes, J. S., Xu, Z.. 2025-11-14. Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae. https://doi.org/10.1101/2025.11.13.688250

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