Complete Telomere-to-Telomere Assembly of the Y Chromosome in the Chinese Quartet

The complete assembly of the human Y chromosome remains a challenge due to its highly repetitive and complex structure. While complete telomere-to-telomere (T2T) assemblies have been generated for a few individuals, such high-quality resources for East Asian populations, particularly for well-characterized multi-omics reference cohorts, are still scarce. The Chinese Quartet, comprising monozygotic twin daughters and their parents, is a premier reference material for genomic studies, yet a T2T-level Y chromosome assembly for this pedigree was lacking. Here, we present a complete, gapless T2T assembly of the Y chromosome (designated CQ-chrY) from the father of the Chinese Quartet. This assembly was generated by integrating Oxford Nanopore ultra-long reads, PacBio HiFi reads, and Hi-C data, resulting in a sequence of 61.88 Mb. The assembly shows exceptional base accuracy (QV = 51.09) and structural completeness (GCI = 100; CRAQ AQI = 95.217). We completely resolved the 33.52 Mb Yq12 heterochromatic region and annotated 164 protein-coding genes and 51.03 Mb (82.47%) of repetitive sequences. This CQ-chrY assembly represents the third complete Chinese Y chromosome and fills the last gap in the T2T assemblies of the Quartet family, providing an invaluable paternal haplotype resource for expanding East Asian genomic standards and for studies on Y chromosome structural variation and evolution.