Untangling the evolutionary history of endogenous retroviruses in anuran genomes

Endogenous retroviruses (ERVs) can represent remnants of past retroviral infections, having associations to disease conditions and pivotal roles in vertebrate genome evolution. The majority of ERV research has had a mammalian focus; anurans (frog and toad species) have comparable genome sizes and number of extant species, yet few ERVs have been described in this order. To untangle the evolutionary history of retroviruses and understand ERVs in non-mammalian genomes, this research explores ERV presence and diversity within and between anuran species. Through designing a similarity-based pipeline, 46 publicly available anuran genomes were screened, identifying 56 novel anuran ERV families. To provide insight into ERV population dynamics within a species, we sequenced and assembled the genomes of two Leptodactylus fallax individuals and identified 22 further novel ERV families, many of which had insertionally polymorphic full-length proviruses with young insertions ages, suggesting recent activity. This is particularly relevant to L. fallax which has experienced severe population declines in the wild (deemed Critically Endangered by the IUCN Red List) and high mortality rates in captivity, with evidence of retroviral involvement in disease. In all anuran genomes, ERV families had characteristics of recent activity (intact genes and little divergence between their long terminal repeats). Through intra- and inter- species ERV screening, I defined an extensive new clade of epsilonretroviruses, possessing a distinctive env gene, prompting a reclassification of previously known amphibian and fish ERVs. I also show ERV-L retrotransposons independently acquired env genes on multiple occasions within anurans, suggesting transitions between LTR retrotransposons and retroviruses. The addition of 78 novel families of ERVs (with multiple genomic loci) identified in anurans also greatly expands the known diversity of ERVs outside of mammals.

Name dc:type.qualificationname

Ph.D

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

Oxford Brookes University

Author dc:creator

• Free, Hayley Beth

Advisors dc:contributor.advisor

• Kanda, Ravinder
• Nichols, Richard
• Cunningham, Andrew

DOI dc:identifier.doi

https://doi.org/10.24384/zpgq-5911

OAI record oai:identifier

https://radar.brookes.ac.uk/radar/oai?verb=GetRecord&metadataPrefix=uketd_dc&identifier=tle%3A2e543531-2353-4b2d-a985-08a87c8a7c0d%3Ad6bd9758-527a-46cd-bfe2-c433766e8fca%3A1