Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat phenotypes are pivotal in facilitating the preservation and utilization of these genetic resources. However, the total genetic diversity within a species can’t be captured by the reference genome of a single individual. The pan-genome is a collection of all the DNA sequences that occur in a species, and it is expected to capture the total genomic diversity of the specific species. We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals, including 723 domestic goats and 90 samples from their wild relatives, which presented a broad regional and global representation. In total, 146 Mb sequences and 974 genes were identified as absent from the reference genome (ARS1.2; GCF_001704415.2). We identified 3,190 novel single nucleotide polymorphisms (SNPs) using the pan-genome analysis. These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives. Presence/absence variation (PAV) analysis revealed gene loss and intense negative selection during domestication and improvement. Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations. It reveals the changes in genomic architecture during goat domestication and improvement, such as gene loss. This improves our understanding of the evolutionary and breeding history of goats.

中文翻译：

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山羊泛基因组揭示了驯化过程中基因丢失的模式


揭示遗传多样性特征并了解不同山羊表型的遗传机制对于促进这些遗传资源的保存和利用至关重要。然而，单个个体的参考基因组无法捕获一个物种内的总遗传多样性。泛基因组是一个物种中出现的所有DNA序列的集合，它有望捕获特定物种的总基因组多样性。我们利用基于图谱到泛的组装技术，基于 813 个个体构建了山羊泛基因组，其中包括 723 只家山羊和来自其野生近缘种的 90 个样本，具有广泛的区域和全球代表性。总共有 146 Mb 序列和 974 个基因被鉴定为参考基因组中缺失（ARS1.2；GCF_001704415.2）。我们利用泛基因组分析鉴定了 3,190 个新的单核苷酸多态性 (SNP)。这些新的 SNP 可以正确揭示家山羊及其野生近缘种的种群结构。存在/不存在变异（PAV）分析揭示了驯化和改良过程中的基因丢失和强烈的负选择。我们的研究强调了山羊泛基因组在捕获缺失遗传变异方面的重要性。它揭示了山羊驯化和改良过程中基因组结构的变化，例如基因丢失。这提高了我们对山羊进化和繁殖历史的了解。