Transposable elements (TE) are one of the major driving forces of genome evolution. Eukaryotic TE evolution can easily be reconstructed thanks to many degraded copies. By contrast, in prokaryotes, TE are considered to be recently acquired, which complicates the study of their dynamics. Insertion sequences (IS) are the most abundant TE in prokaryotes. Models predict a high turn-over that starts by TE acquisition by horizontal transfers, followed by copy number increase and subsequent elimination. In addition, models predict that genomes of intracellular bacteria should have few or no IS. Genome sequencing of obligate intracellular bacteria, as Wolbachia, have questioned models, because some have a considerable abundance of IS. Our work was based on the study of five sequenced Wolbachia genomes. We have realized a detailed IS annotation for each genome. In addition, experimental analyses were performed to test the hypothesis based on in silico analyses. We confirmed that Wolbachia genomes contained a considerable abundance of IS. Surprisingly, the majority of IS copies were degraded, which allowed us to study their evolutionary dynamics. Past IS activity in Wolbachia genomes was not constant during time. We identified phases of high activity alternating with phases of relative quiescence. High activity phases needed to be preceded by horizontal transfers of IS that we experimentally detected in abundance in Wolbachia genomes. Finally, expression analyses suggested that IS activity is not exclusively controlled by IS themselves, but it also depends on the genomic environment of the IS copies.
