BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

中文翻译：

---

国王万岁：使用链接读取、Hi-C 和长读取数据对狮子 (Panthera leo) 进行染色体级组装。


背景 狮子（Panthera leo）是地球上最受欢迎和标志性的猫科动物之一，尽管它很受欢迎，但上个世纪全球狮子数量大幅下降。濒危物种的基因组资源代表了保护领域的重要发展方向，可以对人口学、疾病和种群动态进行高分辨率研究。在这里，我们展示了来自异国猫科动物救援中心（印第安纳州中心点）的圈养非洲狮的染色体水平组装，作为豹属分支唯一社会物种当前和后续遗传工作的资源。结果我们的组装由 10x Genomics Chromium 数据、Dovetail Hi-C 和 Oxford Nanopore 长读数据组成。同线性在狮子、其他豹属基因组和家猫之间高度保守。我们发现狮子基因组中纯合性运行长度的变异性，表明最近可能强烈的近交和瓶颈事件的对比历史。人口统计分析显示，更新世期间所有个体都有相似的古代历史，但亚洲狮除外，亚洲狮的种群规模下降得更快。我们展示了人口统计历史和杂合性推断中参考基因组选择的重大影响。结论我们证明，在比较跨物种杂合性估计时，参考基因组的选择很重要，并且从不同参考推断的杂合性估计不应相互比较。此外，杂合性的估计或纯合性运行的数量或长度不应被视为反映一个物种，因为这些在个体之间可能存在很大差异。 这种高质量的基因组将极大地有助于狮子的持续研究和保护工作，狮子正迅速成为濒临灭绝的物种。