Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

中文翻译：

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改进了国产驴的从头基因组组装。

驴和马的共同祖先可以追溯到大约400万年前。尽管可以在马匹上使用染色体水平的高质量基因组装配体，但目前可用于驴的装配体仅限于中等大小的支架。驴没有更好质量的装配，阻碍了涉及在全基因组范围内表征遗传变异模式的研究。这些范围包括从基因组工具的应用到选择性育种和保存，再到对基础物种形成和驯化的基因组位点进行更基本的表征。我们提供了使用Chicago HiRise组装技术获得的新型高质量驴基因组组装，可提供亚染色体大小的支架。我们利用这种新的装配来获得除马以外的马物种的杂合度的更准确测量值，无论是在全基因组范围内还是在本地，并检测可能与家驴正选择有关的纯合度。最后，这种新的装配使我们能够识别马和驴之间的细小染色体重排，这很可能在它们的分化以及最终形成物种方面发挥了积极作用。