Coevolutionary history of ERVs and Perissodactyls inferred from the retroviral fossil record

• Main Author: Zhu, Henan
• Published: University of Glasgow 2018
• Subjects: QR355 Virology
• Online Access: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.754331

The horse (Equus caballus) is an economically and scientifically important species of mammal. The horse genome (and that of other mammals) contains thousands of sequences derived from retroviruses, called endogenous retroviruses (ERVs). These sequences 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. Horses belong to the family Equidae in the order Perissodactyla - comprising 16 extant species of strict herbivores adapted for running and dietary specialisation. This PhD thesis describes my work developing and applying a novel bioinformatics approach for characterising ERVs. I used this approach to characterise ERVs in genomes of Hippomorpha species in relation to those found in a representative of the Ceratomorpha - the white rhinoceros (Ceratotherium simum). Through comparative analysis of these three genomes, I derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germline. My project has provided an overview of retrotranspositional activity in perissodactyl ERV lineages and identified individual ERV loci that show evidence of involvement in physiological processes and/or pathological conditions. The dataset generated in this project will be of great utility for future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.