Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution

The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. The first telomere-to-telomere haplotype-resolved X chromosome and four autosomes of cattle are presented in a near-complete assembly that is 431 Mb (16%) longer than the current reference genome. The UOA_Wagyu_1 assembly identified 738 new protein-coding genes and supported characterization of centromeric repeats and transposable elements while revealing 49,610 structural variants. The cattle X centromere is a natural neocentromere with highly identical inverted repeats, no bovine satellite repeats, low CENP-A signal, low methylation, and low CpG content, in contrast to the autosomal centromeres that are comprised of typical bovine satellite repeats and epigenetic features. It likely formed from transposable element expansion and CpG deamination, suggesting dynamic evolution. Eighteen X-pseudoautosomal region genes have conserved testes expression between cattle and apes. All cattle X neocentromere protein-coding genes are expressed in testes, which suggest they potentially play a role in reproduction.