Multidimensional telomere diversity and inheritance at individual and population scales

Variation in telomere length, sequence composition and epigenetic state influences genome stability, aging and disease, yet its high-resolution characterization across species remains challenging. Here we present TeloXplorer, a computational framework for long-read data that jointly profiles telomere length, telomere variant repeats (TVRs) and DNA methylation at chromosome-end and haplotype resolution. Across simulated and empirical datasets from humans, Arabidopsis and yeast, TeloXplorer accurately resolved chromosome-end-specific telomere features and highlighted the importance of sample-matched, haplotype-resolved assemblies. Analysis of two human trios revealed concordant relative telomere-length profiles, predominantly Mendelian transmission of TVR haplotypes and family-conserved methylation patterns. Across 232 individuals from the Human Pangenome Reference Consortium, chromosome-end telomere-length rankings were conserved across five continental and 28 population groups. High-accuracy reads from 73 individuals further revealed elevated TVR haplotype diversity among individuals of African ancestry, together with extensive interchromosomal sharing and duplication of TVR architectures. Subtelomeric TAR1 elements were strongly associated with local DNA methylation and telomere motif diversity. Together, these analyses provide a multidimensional atlas of telomere diversity across species, chromosome ends, haplotypes and populations, revealing how telomere architecture varies and is inherited across biological scales.