Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds. Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip. The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.

中文翻译：

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用于山羊遗传和基因组研究的近乎完整的基因组

山羊是最早的家畜之一，在文化和经济上都是世界范围内的重要物种。目前的山羊参考基因组，称为 ARS1，据报道是第一个使用 69x PacBio 测序的非人类基因组组装。然而，ARS1 存在不完整的 X 染色体和高度碎片化的 Y 染色体支架。在这里，我们展示了来自一只雄性 Saanen 奶山羊的非常高质量的从头基因组组装 Saanen_v1，其中第一个山羊 Y 染色体支架基于 117x PacBio 长读长测序和 118x Hi-C 数据。由于在三分之二的常染色体的近端和远端存在着丝粒和端粒重复序列，并且间隙数量大大减少（169 对 773），Saanen_v1 显示出高度的完整性。Saanen_v1 基因组组装的完整性和准确性也通过染色体上更多的组装序列（Saanen_v1 为 2.63 Gb，ARS1 为 2.58 Gb）、转录组数据的映射比率略有增加以及更多基因锚定到染色体上得到证实。在 ARS1 中发现的 8 个假定的大组装错误（每个 1 到 ~ 7 Mb）被修正，并且首次估计了该反刍动物 Y 染色体的替换率。此外，与 ARS1 相比，Saanen_v1 中的序列改进使我们能够为广泛使用的 GoatSNP50 芯片中 4.4% 的单核苷酸多态性 (SNP) 探针分配可能的正确位置。