Abstract

Ongoing efforts to improve sheep reference genome assemblies still leave many gapsand incomplete regions, resulting ina few common failuresand errors in genomic studies. Here, we reporta 2.85-Gb gap-free telomere-to-telomere genome of a ram ( T2T-sheep1.0), including all autosomesand the X andY chromosomes. This genome adds 220.05 Mb of previously unresolved regions and 754 new genestothe most updated reference assembly ARS-UI_Ramb_v3.0; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. T2T-sheep1.0 has abase accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against T2T-sheep1.0 identifies 2,664,979 new single-nucleotide polymorphismsin previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example,ABCC4) and wool fineness (for example, FOXQ1).

nature genetics

DOI:https://doi.org/10.1038/s41588-024-02037-6