Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained as living stocks and distributed to academic investigators, is missing. In the present study we surveyed two populations of P. maniculatus that are maintained at the Peromyscus Genetic Stock Center (PGSC) for polymorphisms across their 2.5 × 109 bp genome. High density of variation was identified, corresponding to one SNP every 55 bp for the high altitude stock (SM2) or 207 bp for the low altitude stock (BW) using snpEff (v4.3). Indels were detected every 1157 bp for BW or 311 bp for SM2. The average Watterson estimator for the BW and SM2 populations is 248813.70388 and 869071.7671 respectively. Some differences in the distribution of missense, nonsense and silent mutations were identified between the stocks, as well as polymorphisms in genes associated with inflammation (NFATC2), hypoxia (HIF1a) and cholesterol metabolism (INSIG1) and may possess value in modeling pathology. This genomic resource, in combination with the availability of P. maniculatus from the PGSC, is expected to promote genetic and genomic studies with this animal model.

中文翻译：

---

圈养鹿鼠（Peromyscus maniculatus）群体的基因组变异

鹿鼠（Peromyscus）是北美最常见的啮齿动物。尽管某些物种有参考基因组，但缺乏全面的多态性数据库，特别是那些作为活体种群饲养并分发给学术研究人员的多态性数据库。在本研究中，我们调查了 Peromyscus 遗传库存中心 (PGSC) 保存的两个 P. maniculatus 种群，了解其 2.5 × 109 bp 基因组的多态性。使用 snpEff (v4.3) 识别出高密度变异，对应于高海拔种群 (SM2) 每 55 bp 一个 SNP，或低海拔种群 (BW) 每 207 bp 一个 SNP。BW 每 1157 bp 检测一次插入缺失，SM2 每 311 bp 检测一次插入缺失。BW 和 SM2 群体的平均 Watterson 估计量分别为 248813.70388 和 869071.7671。在不同种群之间发现了错义、无义和沉默突变分布的一些差异，以及与炎症 (NFATC2)、缺氧 (HIF1a) 和胆固醇代谢 (INSIG1) 相关的基因多态性，可能在病理学建模中具有价值。该基因组资源与 PGSC 提供的 P. maniculatus 相结合，预计将促进该动物模型的遗传和基因组研究。