Background Vertebrate 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. Results We 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. Conclusions Sequence 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. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
27Mammalian genomes contain a fossilized record of ancient retroviral infections in the form of 28 endogenous retroviruses (ERVs). We used whole genome sequence data to assess the origin 29 and evolution of the recently active ERV-Fc gammaretroviral lineage based on the record of past 30 infections retained in the genome of the domestic dog, Canis lupus familiaris. We identified 165 31 loci, including 58 insertions absent from the dog reference assembly, and characterized element 32 polymorphism across 332 canids from nine species. Insertions were found throughout the dog 33 genome including within and near gene models. Analysis of 19 proviral sequences identified 34 shared disruptive mutations indicating defective proviruses were spread via complementation. 35
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