Final Report Summary - GENOVIR (Adaptation of Virus Genomes to Insect Immunity) At the frontier of ecology and genomics, the GENOVIR project took on the challenge of studying ecological adaptation at the level of whole genomes. Cutting-edge genomics applied to the interface of ecology broaden our understanding of evolutionary processes. How ecology shapes genomes? In theory, species evolve as groups of genomes adapting to particular ecological niches. Thus, shifts to a new ecological niche should be connected to genome divergence, and ultimately to the making of new species. The recent development in sequencing technology seeded the emergence of the new field of ecological genomics, by lifting the difficulty of simultaneously studying evolution at both ecological and whole genome levels. Insect viruses were chosen to study how ecological adaptation affects genomes because their ecological niches are defined by their hosts and because of their relatively small genomes. Phylogenomic analyses showed several families of insect large DNA viruses formed a group that first evolved in the Paleozoic era, in the same period as their insect hosts. The long co-evolutionary history between insect DNA viruses and theirs hosts allows the investigation of the question of genome adaptation at different time scales from a micro- to macro-evolutionary perspective. The transmission of baculoviruses as groups of genomes sets them apart for studying the effect of niches on populations and for linking genome changes to ecological changes. Large-scale experimental evolution followed by ultra-deep sequencing was performed to study the effect of niche specialization on viral populations. This further allowed the study of rare mutations, such as those resulting for horizontal gene transfers from the host to the virus during infection. Polydnaviruses have extraordinary genomes, domesticated by wasps to deliver molecular weapons to fight the immunity of their Lepidoptera hosts. The genomes of polydnaviruses, associated with parasitic wasps adapted to different hosts, were sequenced to study how the ecology of the wasp changed viral genomes in this mutualistic model. We found that depending on the ecological context different polydnavirus genes were under selection implying the strong role of the virus for the diversification of their carrier wasps. Lastly, the diversity of insect viruses provided an exceptional opportunity to examine if different evolutionary lineages, such as baculoviruses and entomopoxviruses, have converged toward similar genomic solutions to respond to similar immunity. In contrast, the particular cell fusion protein complex (pifs) found in insect large DNA viruses are derived from a common ancestor and has been conserved since distant evolutionary past.Altogether by studying the evolution of insect viruses, GENOVIR found that indeed adaptation to particular ecological niches leads to genomic divergence.
