BackgroundVertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids.ResultsWe identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations.ConclusionsSequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs.

中文翻译：

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家养和野生犬科动物内源性伽马逆转录病毒谱系的起源和近期扩展

背景脊椎动物基因组包含侵入祖先宿主生殖系并作为内源性逆转录病毒 (ERV) 传递给后代的逆转录病毒的记录。ERV 会影响宿主功能，因为它们包含在宿主内表达所需的序列。狗是研究疾病和进化的重要系统，但尚无关于狗感染性逆转录病毒的证实报告。在这里，我们利用 Illumina 全基因组序列数据来评估家养和野生犬科动物中最近活跃的伽马逆转录病毒谱系的起源和进化。结果我们在犬科动物中鉴定了许多最近整合的犬科动物特异性 ERV-Fc 亚谱系的基因座，包括 58 个插入不存在于参考程序集中。在整个狗基因组中发现了插入，包括基因模型内和基因模型附近。通过直系同源占据位点的比较，我们表征了 332 个基因组中的元素流行率，包括所有 9 个现存犬科动物物种，揭示了物种和亚群之间 ERV-Fc 分离的进化模式。结论序列分析揭示了常见的破坏性突变，表明 ERV-Fc 的主要形式Fc 通过有缺陷的原病毒的反式互补传播。ERV-Fc 活动包括多种循环变异，这些变异感染了过去 2000 万到 160 万年内的犬科动物祖先，最近在亚谱系中爆发了导致狼和狗的种系入侵。结论序列分析揭示了常见的破坏性突变，表明通过有缺陷的原病毒的反式互补传播的主要形式的 ERV-Fc。ERV-Fc 活动包括多种循环变异，这些变异感染了过去 2000 万到 160 万年内的犬科动物祖先，最近在亚谱系中爆发了导致狼和狗的种系入侵。结论序列分析揭示了常见的破坏性突变，表明通过有缺陷的原病毒的反式互补传播的主要形式的 ERV-Fc。ERV-Fc 活动包括多种循环变异，这些变异感染了过去 2000 万到 160 万年内的犬科动物祖先，最近在亚谱系中爆发了导致狼和狗的种系入侵。