It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.

中文翻译：

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基因组共线性分析阐明了奇蹄类动物中驴 1 号染色体和马 5 号染色体的进化：一项比较研究

解决物种基因组的进化历史非常重要，因为它影响了基因组组织和染色体结构。测序技术的快速创新和组装算法的改进使得高度连续的基因组的创建成为可能。DNA Zoo 是一家致力于动物保护的全球组织，提供超过 150 个染色体长度的基因组组装。该数据库在比较基因组学领域具有巨大的潜力。以DNA Zoo提供的驴（Equus asinus asinus，EAS）基因组为例，支架N50长度和Benchmarking Universal Single-Copy Ortholog评分分别达到95.5 Mb和91.6%。我们确定了细胞遗传学命名法，纠正了驴基因组染色体长度序列的方向，分析了驴和马之间的全基因组染色体重排，并说明了奇蹄类中驴1号染色体和马5号染色体的进化。DNA Zoo提供的驴基因组具有较好的连续性和完整性。基于序列的比较基因组分析对于染色体进化研究很有用。先前发表的几个染色体涂色结果可用于识别细胞遗传学命名法并纠正新组件的染色体长度序列的方向。与马基因组相比，驴的1、4、20、X染色体有几个明显的倒位，与之前的研究结果一致。4.8 Mb的倒置结构首次在驴25号染色体和平原斑马11号染色体中发现。我们推测马31号和4号染色体的倒置结构和串联融合是非马科动物的共同特征，这支持了该研究的正确性。现有的马属系统发育在一定程度上。