A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Recent advances in sequencing technologies have enabled the complete assembly of human genomes from telomere to telomere (T2T), resolving previously inaccessible regions such as centromeres and segmental duplications. While T2T assemblies of the Chinese population (e.g., T2T-CN1 and T2T-YAO) have been reported, haplotype-resolved familial genomes—critical for studying inheritance patterns and structural variation—remain unexplored. Here, we present a high-quality, haplotype-phased T2T assembly of the Chinese Quartet (T2T-CQ), a family cohort comprising monozygotic twins and their parents, generated using high-coverage ultra-long Nanopore and high-fidelity sequencing. The T2T-CQ assembly achieves haplotype quality values exceeding 70, comparable to the T2T-CHM13 reference, enabling comprehensive annotation of centromeric regions. Our analysis reveals novel higher-order repeat (HOR) patterns, including expanded and contracted HOR arrays, shedding light on the dynamic nature of centromere evolution. Furthermore, through haplotype-resolved assembly and comparative analysis of the complete centromeric sequences between the twins, we identify potential copy number variations in HOR structures, with distinct patterns differentiating maternal and paternal inheritance. This work not only provides a critical genomic resource for the Han Chinese population but also establishes a foundation for forensic identification and complex case resolution. Additionally, our dataset contributes to the construction of a T2T pan-Chinese reference genome, facilitating future studies on population-specific structural variations and centromere biology.