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Horizontal transfers (HTs) of genetic material is increasingly recognized as a major force shaping genomic evolution in some eukaryotes, but the mechanisms underlying these HTs are still unknown. lt has been proposed that viruses cou Id act as vectors of HT. Accordingly, we recently uncovered many host sequences, mostly transposable elements (TEs) integrated into AcMNPV baculovirus genomes using short read sequencing of AcMNPV particles extracted from the beet armyworm Spodoptera exigua. Here we further characterize the structure and full diversity of moth sequences carried by AcMNPV genomes using long-read sequencing. We detected no less than 68,375 host sequences integrated in AcMNPV genomes, among which are 30,196 transposable elements (TEs). We found ail DNA TEs and LTR retrotransposons superfamilies previously identified using short read sequencing, as well as additional DNA TE and autonomous and non-autonomous non-L TR superfamilies. Expected target site duplication motifs cou Id be identified for all these superfamilies, showing that bona fide transposition is the main mechanism underlying TE integration into viral genomes. lnterestingly, the long read sequencing approach allowed us to show that a single viral genome may transport more than one host sequence. Our study of non-TE sequences is also revealing that host genes can jump into viral genomes du ring a single round of infection. Overall, our results suggest that about a quarter of AcMNPV genomes harbor at least one host sequence in AcMNPV populations, further supporting the raie of viruses as vectors of HT between insects. We are currently characterizing in details the structure and genomic distribution of these insertions a long the viral genome.

Genetie variation underpins the evolutionary process of adaptation. As populations become adapted to different environments, they diverge from one another. Baculoviruses infecting different hast species thus usually belong to different species. Yet some viruses, such as Autographa californica multiple Nucleopolyhedrovirus (AcMNPV), have retained the capacity of infecting many hast species. To understand how AcMNPV cou Id draw on standing genetic variation to adapt to different host species we undertook an experimental evolution protocol. A highly polymorphie AcMNPV population was ta ken through 10 in vivo infection cycles in 4 host species of various susceptibilities, to create 50 evolutionary lines in which the virus was allowed to evolve either as specialist on separate species (4x10 lines) or as generalist on all the hasts (10 lines), whereby the viral population resulted from the infection of all hasts at each generations. We then characterized the genetic make up of the original and evolved baculovirus populations by ultra-deep Illumina sequencing. Using a population genomics approach, we then estimated the global fitness and genetic diversity of each of the evolved populations and their divergence from one another. We found that the specialist lines that evolved on the same host species were more similar to one another than to other lines, especially in the most susceptible hosts, showing experimental evolution cou Id lead to specific adaptation. Furthermore, we found a general diminution of genetic diversity in the specialist lines compared to the ancestral population. The viral lines that cou Id adapt to more resistant host retained higher genomic diversity than those that did not, showing genetic variation is an important component of baculovirus adaptation. Evolution in all the hosts led to high genetic diversity in the generalist lines, which cou Id foster ecological resilience in variable environments such as those encountered by the virus in natural landscapes.

Le colloque de Génomique Environnementale (GE) est une manifestation nationale permettant aux chercheurs français et internationaux travaillant sur l’écologie, l’évolution de la biodiversité ou le fonctionnement des écosystèmes d’échanger sur l’utilisation des nouvelles technologies de séquençages (NTS) et des développements récents en bioinformatique. Il s’agit de la quatrième édition du colloque de Génomique Environnementale après Lyon (2011), Rennes (2013) et de Montpellier (2015) organisé sous l'égide du GDR "Génomique Environnementale" (http://gdr3692.wix.com/gdrge) dont les actions sont soutenues par le CNRS, l’INRA et le MNHN. Ce colloque représente une opportunité exceptionnelle pour échanger entre chercheurs/doctorants/post-doctorants et répondre aux défis posés en matière d’environnement, de réchauffement climatique et plus généralement de maîtrise des impacts globaux sur les écosystèmes. Le colloque GE est un lieu d’échanges privilégié permettant un dialogue efficace entre, d’une part, la communauté scientifique et, d’autre part, les acteurs gérant les systèmes d’observation et d’analyse des écosystèmes (zones ateliers, ORE, parcs naturels etc...) ou les demandes sociétales dont les entreprises sont souvent porteuses.