A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

完整的山羊 （Capra hircus） 参考基因组增强了对遗传变异的分析，从而为山羊和相关物种的驯化和选择提供了见解。在这里，我们从绒山羊 （T2T-goat1.0） 组装了一个端粒到端粒 （T2T） 无间隙基因组 （2.86 Gb），包括 20.96 Mb 的 Y 染色体。T2T-goat1.0 的碱基准确度为 >99.999%，可纠正先前组装中的许多全基因组结构和碱基错误，并将 288.5 Mb 先前未解析的区域和 446 个新组装的基因添加到参考基因组中。我们对 PacBio 读数的五个代表性山羊品种的基因组进行了测序，并使用 T2T-goat1.0 作为参考来识别总共 63,417 个结构变异 （SV），其中多达 4711 个 （7.42%） 在先前未解析的区域。T2T-goat1.0 应用于全球野生和家养山羊的种群分析，揭示了 32,419 个 SVs 和 25,397,794 个 SNP，其中包括 870 个 SVs 和 545,026 个 SNP，位于以前未解析的区域。此外，我们的分析揭示了一组与驯化（例如 NKG2D 和 ABCC4）和羊绒性状（例如 ABCC4 和 ASIP）相关的选择性变异和基因。