The complete telomere-to-telomere sequence of a mouse Y chromosome.

The mouse Y chromosome is essential for male reproduction, yet the GRCm39 reference contains 25 gaps, particularly in repetitive and complex regions. Here, we assembled a telomere-to-telomere Y chromosome (mT2T Y) of 95.21 Mb from a C57BL/6 mouse incorporating parental genomes. This assembly fills all gaps, corrects structural errors, and adds over 8.70 Mb of previously unassembled sequence to the reference genome. We annotated 142 previously unidentified genes, identified Y specific satellite arrays, and mapped homologous recombination loci in the pseudoautosomal region (PAR). Analysis of X Y homologous gene expression revealed a Y chromosome dosage compensation mechanism. By combining mT2T Y with T2T mhaESC, we completed the T2T assembly of all C57BL/6 chromosomes, designated T2T mhaESC+Y, providing a complete C57BL/6 reference genome.