Thesis defence Marie Verneret

Composition of the jury:

Carole CHARLIER - Reviewer
Professeur associée, Université de Liège, GIGA

Anna-Sophie FISTON-LAVIER - Reviewer

Professeure, Université de Montpellier, ISEM

Clément GILBERT - Examiner
Directeur de recherche, CNRS, EGCE

Julien THEZE - Examiner
Chargé de recherche, INRAE, EPIA

Sébastien DEVILLARD - Examiner
Professeur, Université Lyon 1, LBBE 

Jocelyn TURPIN - Thesis supervisor
Chargé de recherche, INRAE, IVPC 

Emmanuelle LERAT - Thesis supervisor
Chargée de recherche, CNRS, LBBE

Caroline LEROUX - Thesis co-superviser
Directrice de recherche, INRAE, IVPC

Abstract:

In most mammals, endogenous retroviruses (ERVs) represent a major component of the genome, often more abundant than protein-coding genes. Derived from ancient retroviral infections integrated into the germline, ERVs are transmitted vertically and represent lasting traces of virus-host interactions. While most of the exogenous retroviruses that gave rise to these insertions have disappeared, small ruminants are an exceptional case: some ERVs still coexist with their exogenous counterparts responsible for respiratory cancers. This makes them a valuable model for studying host–retrovirus coevolution and the boundaries between endogenous and exogenous forms.

This thesis aims to trace the evolutionary history and diversity of ERVs in sheep and goats, which are closely related species but with distinct evolutionary trajectories. I analyzed a large collection of genomic data, combining reference genomes and population-level datasets from several hundred individuals.

The first part of the thesis focuses on characterizing all ERV families present in the reference genomes of wild and domestic sheep and goats. This analysis enriched the known ERV repertoire and revealed families shared among small ruminants, shaped by multiple waves of endogenization over the last 40 million years, with dynamics differing between species and families. Some families show signatures of recent transposition activity, notably family II-5, closely related to currently circulating oncogenic exogenous retroviruses.

The second part investigates insertional polymorphism within sheep and goat populations. While most insertions are ancient and fixed, three families, including II-5, display low-frequency insertions, confirming their recent mobilization.

By combining comparative and population-level analyses, this thesis highlights the diversity, dynamics, and persistence of endogenous retroviruses in small ruminants. It shows that some ERV families remain potentially active emphasizing the role of ERVs in genome evolution and the complex interplay between endogenous and exogenous retroviruses.