Comparative analysis of GRCh38 and Telomere-to-Telomere (T2T) Human Genome Assemblies Reveals Novel Insights into Telomere Architecture

Accurate characterisation of human telomeres has been historically constrained by limitations in the GRCh38 reference genome, with thousands of missing regions, particularly at the chromosome termini. These gaps limit the ability to detect meaningful inter-individual variation in telomeric architecture. Recent completion of T2T-CHM13 assembly overcomes these limitations, providing uninterrupted telomeric, subtelomeric sequences that enable the precise measurement of telomere repeat structure and length. Telomere motif, as assessed by T2T data, was generally highly dense between 2 and 6kb at each chromosome end, with considerable asymmetry between the two arms of the same chromosome. Overall, a comparison between GRCh38p14 and T2T-CHM13v2.0 reveals strong concordance, but frameshifts, corrected sequence gaps, and improved continuity in T2T firmly establish it as a much more complete representation of the human genome. The T2T assembly also reveals an interesting, highly GC-dense region along with a specific motif at the telomere-subtelomere boundary that appears to be a feature not reliably captured in the incompletely tiled GRCh38 reference. We were also able to detect a specific AT-rich motif, which is excluded from the terminal regions of the chromosomes. Such key telomeric signatures could have functional implications for the structural stability and regulation of chromosome ends.