2025/06/15 by Zikun Yang, Shilong Zhang, Glennis A. Logsdon +1 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Genetic Mapping and Diversity in Plants and Animals #Fungal and yeast genetics research #RNA and protein synthesis mechanisms
paper · doi:10.1101/2025.06.15.659631
openalex publication_date 2025/06/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22
Abstract Tandem repeats (TRs) are pervasive in eukaryotic genomes and play key roles in genome organization, evolution, and function, particularly in complex regions such as centromeres and subtelomeres. Although long-read sequencing technologies have improved the resolution of these regions, existing methods remain limited in their ability to systematically and accurately characterize large-scale TRs. Here, we introduce VAMPIRE, a k-mer–based computational tool for comprehensive TR discovery, annotation, and quantification. Unlike previous methods, VAMPIRE enables reference-free, fine-grained decomposition of both simple and complex TRs, capturing motif variation in sequence, length, and structure with high sensitivity and scalability. Applied to complete telomere-to-telomere (T2T) human and nonhuman primate (NHP) genome assemblies, VAMPIRE reveals previously unrecognized high-order repeat inversions within human centromeres—an underappreciated evolutionary mechanism contributing to centromere diversity. Additionally, the tool identifies lineage-specific and expanded TRs, including human-specific STR/VNTR expansions and NHP-specific subtelomeric heterochromatin (e.g., pCht/StSat), underscoring their dynamic turnover and structural complexity. VAMPIRE provides a robust and scalable framework for TR analysis in the era of long-read sequencing, with broad utility across human genetics, evolutionary biology, and the study of complex TRs in non-model organisms.