Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia.
Department of Integrative Biology, University of South Florida, Tampa, FL.
Genome Biol Evol. 2020 May 1;12(5):618-625. doi: 10.1093/gbe/evaa069.
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.
草原犬鼠（Cynomys 属）是美国西部的标志性动物。它们庞大的群居性和复杂的叫声数十年来一直是科学和大众关注的焦点。大量文献记录了它们在北美西部草原作为关键物种的作用：它们为其他脊椎动物创造栖息地，增加植物的养分可用性，并作为哺乳动物、爬行动物和鸟类捕食者的食物来源。另一个关键作用在于它们对森林鼠疫（由鼠疫耶尔森氏菌引起）的极度易感性，这导致了它们的种群周期性灭绝，从而在生物群落和生态过程中产生时空异质性。在这里，我们报告了科罗拉多州特柳赖德市（美国）的格氏草原犬鼠（C. gunnisoni gunnisoni）的第一个 Cynomys 基因组。该基因组是使用 PacBio 和 Illumina reads 的混合组装构建的，并使用 MaSuRCA 和 PBJelly 进行组装，得到的支架 N50 为 824kb。总基因组大小为 2.67Gb，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同源物数据库恢复了 94.9%（91%完整）的单拷贝直系同源物，并检测到 49,377 个基因模型（332,141 个编码区）。成对顺序马尔可夫合并显示出长期稳定的种群大小的支持，随后在更新世末期附近开始稳定下降，以及最近的种群减少。该基因组将有助于研究哺乳动物进化、疾病抗性以及地松鼠生活史特征的基因组基础。
