A near-complete quail genome identifies heterochromatin expansion and chromosome architecture remodeling.

Avian genomes are typically compact, with limited repetitive content, but the Japanese quail (Coturnix japonica) represents an exception. Here, we report a near-complete chromosome-level quail genome assembly (1.33 Gb), up to 43% larger than previous quail assemblies. The assembly reveals extensive repeat accumulation and heterochromatin expansion, particularly in the pericentromeric regions of micro- and dot chromosomes, and identifies a conserved centromeric repeat shared across chromosomes. Comparative analyses show that transposable element accumulation reshaped chromatin architecture, histone modification landscapes, and interchromosomal interactions. The female-specific W chromosome underwent extensive heterochromatinization and gene degeneration. Integrated epigenomic profiling further identifies quail-specific chromatin states. These findings reveal quail-specific heterochromatin expansion and provide new insights into avian centromere evolution, heterochromatin biology, and sex chromosome remodeling.