Endogenous viral sequences are essentially 'fossil records' that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements (GRD) and the geminivirus-like elements (EGV) found respectively within the nuclear genomes of several Nicotiana species and various Dioscorea spp. of the Enantiophyllum clade. Those two new classes of endogenous plant virus sequence are apparently derived from ancient geminiviruses in the genus Begomovirus. GRD and EGV sequences likely became integrated millions years ago. Interestingly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. We recently found using in silico searches that other ssDNA virus-like sequences are included within complete or draft genomes of various plant species, including apple tree (Malus domestica), black cottonwood (Populus trichocarpa), various Coffea spp, eggplant (Solanum melongena), lettuce (lactuca sativa), and Tepary bean (Phaseolus acutifolius), which suggests that endogenous geminiviruses may be more common in plant genomes than has previously been appreciated. (Texte intégral)