Abstract
Endogenous viral elements (EVEs) are nucleic sequences of viral origin that have integrated into the genome of their hosts through passive or active horizontal gene transfer (HGT) mechanisms. They constitute molecular fossils that provide access to viral sequences up to several million years old and potentially allow the reconstruction of the evolutionary history of entire viral lineages using paleovirological approaches. The majority of known plant EVEs are derived from viruses with a DNA genome of the Caulimoviridae family. They are present in the genome of a large number of vascularized plants, from the most basic to the most advanced, and most of them correspond to fossil viruses that do not belong to any existing viral genus. The work reported in this thesis first focused on the search for infectious forms of a florendovirus and a petuvirus that are known only as (fossil) EVEs, using the Citrus genetic resources conserved by CIRAD in Guadeloupe and molecular and immuno-molecular approaches. Our results confirmed that the expression of infectious EVEs in plants is tightly regulated. Using in silico approaches, 50 co-transcripts comprising Caulimoviridae and plant sequences were identified in 45 lycophyte, fern, gymnosperm and angiosperm species, providing evidence for the integration of Caulimoviridae coding sequences in plant genes. The study of badnavirus EVEs in a resistance gene (R1) to Phytophtora infestans in several eggplant species and in R1 orthologs in related Solanum species showed that some insertions led to alternative splicing and provided evidence for the acquisition of an alternative promoter of badnaviral origin. This study also demonstrated for the first time the presence of badnaviruses in Solanaceae hosts. Using paleovirological approaches, we reassessed the host range and diversity of the Caulimoviridae through the discovery of several new but probably fossilized viral genera. Our work also provided insights into the role of host swaps and the acquisition of new genes during the evolution of the Caulimoviridae.