Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison’s prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.

中文翻译：

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甘尼森草原土拨鼠（Cynomys gunnisoni）的第一个基因组序列，是基石物种，是鼠疫鼠疫的传播者。

草原土拨鼠（Cynomys属）是美国西部的一种有魅力的象征。几十年来，他们庞大的社会群体和复杂的声音一直是科学和大众关注的主题。大量文献证明了它们作为北美西部草原的主要物种的作用：它们为其他脊椎动物创造了栖息地，增加了植物的营养供应，并为哺乳动物，鳞状和鸟类掠食者提供了食物。另一个主要的作用在于它们对鼠疫鼠疫的极度易感性（由鼠疫耶尔森氏菌引起），导致种群周期性灭绝，从而在生物群落和生态过程中产生时空异质性。在这里，我们报告第一个Cynomys甘尼森草原土拨鼠（C. gunnisoni gunnisoni）（来自美国科罗拉多州的特柳赖德）。该基因组是使用PacBio和Illumina读物的混合组件构建的，并与MaSuRCA和PBJelly组装在一起，从而产生了824 kb的支架N50。基因组总大小为2.67 Gb，其中32.46％的碱基位于重复区域。我们使用哺乳动物基准通用单拷贝直系同源物数据库检索了94.9％（完整的91％）直系同源物，并检测到49,377个基因模型（332,141个编码区）。成对的顺序马尔可夫联盟显示出对长期稳定的人口规模的支持，随后在更新世末期开始稳步下降，以及最近的人口减少。该基因组将有助于研究哺乳动物的进化，抗病性以及地松鼠生活史特征的基因组基础。