Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes

J Virol. 2018 Nov 12;92(23):e00927-18. doi: 10.1128/JVI.00927-18. Print 2018 Dec 1.


The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.

Keywords: endogenous; equid; evolution; horse; perissodactyl; retrovirus; rhinoceros.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Lineage
  • Computational Biology
  • Endogenous Retroviruses / classification*
  • Endogenous Retroviruses / genetics*
  • Endogenous Retroviruses / isolation & purification
  • Evolution, Molecular*
  • Genetic Variation*
  • Genome*
  • Genomics
  • Horses / genetics
  • Horses / virology*
  • Perissodactyla / genetics
  • Perissodactyla / virology
  • Phylogeny
  • Retroviridae Infections / veterinary*
  • Retroviridae Infections / virology
  • Sequence Homology
  • Transcriptome