Natacha Kremer

Transposable elements (TEs) are widespread genomic parasites, whose activity is largely restrained by RNA interference pathways. Some of these pathways also contribute to antiviral immunity, allowing a mechanistic overlap that could generate interactions—or even trade-offs—between TE repression and viral defense. Here, we investigated this interplay by experimentally infecting two strains of Drosophila melanogaster and Drosophila simulans with three distinct viruses: Drosophila X virus (DXV), Flock House virus (FHV), and Invertebrate Iridescent virus 6 (IIV6). Through deep RNA-seq and small RNA-seq analyses, we show that viral infection consistently alters TE transcript abundance, although the direction and magnitude of these changes strongly depend on both the host strain and the virus. In addition, we provide an in-depth characterization of the dynamic TE repertoire that IIV6 carries. IMPORTANCE: Transposable elements (TEs) are genomic parasites that are found in all genomes. Here, using two strains of Drosophila and three viruses, we show that viral infections consistently affect TE transcript amounts. However, the magnitude and direction of the TE modulation depend on the host strain, the virus, and the tissue. In addition, one of the viruses under study, the Invertebrate Iridescent virus 6 (IIV6), carries TEs on its own, which we characterize as a dynamic repertoire.

Les associations entre organismes eucaryotes et micro-organismes sont fréquemment observées dans la nature et s’étendent le long du continuum parasitisme-mutualisme. Si de nombreuses associations symbiotiques ont été bien caractérisées, leur mise en place et leur évolution ont été rarement étudiées. Les bactéries intracellulaires Wolbachia induisent des effets très différents, variant du parasitisme de la reproduction chez les Arthropodes au mutualisme chez les Nématodes. Nous nous sommes ici intéressés à l’hyménoptère Asobara tabida, rare espèce où Wolbachia est obligatoire pour l’ovogenèse de son hôte Arthropode, de façon à étudier les mécanismes à l’origine d’une transition évolutivement récente. Nous avons tout d’abord étudié la variabilité de la dépendance vis-à-vis de Wolbachia au sein du genre Asobara. Par diverses approches de transcriptomique, nous avons ensuite caractérisé les mécanismes moléculaires impliqués dans la dépendance chez A. tabida, et mis en évidence des processus impliqués dans la mort cellulaire programmée, l’immunité (sens large) et le développement. Enfin, nous avons étudié l’impact de Wolbachia sur la physiologie de son hôte, en étudiant le métabolisme du fer et plus généralement l’immunité dans diverses associations symbiotiques. Ces études montrent que la dépendance n’est pas forcément associée à l’apport de nouvelles fonctions et pourrait au contraire être le reflet de processus compensatoires mis en place par l’hôte, en réponse aux perturbations physiologiques induites par le symbiote. Ces résultats appellent à considérer les effets et les conséquences de ces symbiotes au delà des mécanismes qui permettent leur maintien dans les populations

A particularly well-studied evolutionary model is the vinegar fly Drosophila melanogaster, a cosmopolitan insect of ancestral southern-central African origin. Recent work suggests that it expanded out of Africa ∼9,000 years ago, and spread from the Middle East into Europe ∼1,800 years ago. During its global expansion, this human commensal adapted to novel climate zones and habitats. Despite much work on phenotypic differentiation and adaptation on several continents (especially North America and Australia), typically in the context of latitudinal clines, little is known about phenotypic divergence among European populations. Here, we sought to provide a continent-wide study of phenotypic differentiation among European populations of D. melanogaster. In a consortium-wide phenomics effort, we assayed 16 fitness-related traits on a panel of 173 isofemale lines from 9 European populations, with the majority of traits measured by several groups using semi-standardized protocols. For most fitness-related traits, we found significant differentiation among populations on a continental scale. Despite inevitable differences in assay conditions among labs, the reproducibility and hence robustness of our measurements were overall remarkably good. Several fitness components (e.g., viability, development time) exhibited significant latitudinal or longitudinal clines, and populations differed markedly in multivariate trait structure. Notably, populations experiencing higher humidity/rainfall and lower maximum temperature showed higher viability, fertility, starvation resistance, and lifespan at the expense of lower heat-shock survival, suggesting a pattern of local adaptation. Our results indicate that derived populations of this tropical fly have been shaped by pervasive spatially varying multivariate selection and adaptation to different climates on the European continent.

Transposable elements (TEs) are parasite DNA sequences that are controlled by RNA interference pathways in many organisms. In insects, antiviral immunity is also achieved by the action of small RNAs. In the present study, we analyzed the impacts of an infection with Drosophila C Virus (DCV) and found that TEs are involved in a dual response: on the one hand TE control is released upon DCV infection, and on the other hand TE transcripts help the host reduce viral replication. This discovery highlights the intricate interactions in the arms race between host, genomic parasites, and viral pathogens. Significance statement: Transposable elements (TEs) are widespread components of all genomes. They were long considered as mere DNA parasites but are now acknowledged as major sources of genetic diversity and phenotypic innovations. Using Drosophila C virus, here we show that TEs are at the center of defense and counter-attack between host and virus. On the one hand, TE control is released upon viral infection, and on the other hand, TE transcripts help the host reduce viral replication. To our knowledge, this is the first time such a complex host-pathogen interaction involving TEs is shown.

Symbiosis is a continuum of long-term interactions ranging from mutualism to parasitism, according to the balance between costs and benefits for the protagonists. The density of endosymbionts is, in both cases, a key factor that determines both the transmission of symbionts and the host extended phenotype, and is thus tightly regulated within hosts. However, the evolutionary and molecular mechanisms underlying bacterial density regulation are currently poorly understood. In this context, the symbiosis between the fruit fly and its intracellular bacteria Wolbachia (wMelPop strain) is particularly interesting to study. Although vertically transmitted, the symbiont is pathogenic, and a positive correlation between virulence and wMelPop density is observed. In addition, the number of repeats of a bacterial genomic region -Octomom- is positively correlated with Wolbachia density, underlying a potential genetic mechanism that controls bacterial density. Interestingly, the number of repeats varies between host individuals, but most likely also within them. Such genetic heterogeneity within the host could promote conflicts between bacteria themselves and with the host, notably by increasing within-host competition between symbiont genotypes through a process analogous to the tragedy of the commons. To characterize the determinisms at play in the regulation of bacterial density, we first introgressed wMelPop in different genetic backgrounds of D. melanogaster, and found different density levels and Octomom copy numbers in each host lineage. To determine whether such variations reflect a host genetic determinism on density regulation through Octomom copy number selection, we replicated the introgressions and performed reciprocal crosses on the two Drosophila populations with the most extreme density levels. In both experiments, we detected an absence of directionality in the patterns of infection, associated with a strong instability of these patterns across generations. Given that bacterial density was highly correlated with Octomom copy numbers in all experiments, these results rather suggest a strong influence of drift and a random increase in the frequency of certain bacterial variants. We then discuss how drift, both on the symbiont population during transmission and on the host population, could limit the efficiency of selection in such a symbiotic system, and the consequences of drift on the regulation of density and composition of bacterial populations.

Evolutionary theory predicts that vertically transmitted symbionts are selected for low virulence, as their fitness is directly correlated to that of their host. In contrast with this prediction, the Wolbachia strain wMelPop drastically reduces its Drosophila melanogaster host lifespan at high rearing temperatures. It is generally assumed that this feature is maintained because the D. melanogaster-wMelPop symbiosis is usually not exposed to environmental conditions in which the symbiont is virulent. To test this hypothesis, we submitted wMelPop-infected D. melanogaster lines to 17 generations of experimental evolution at a high temperature, while enforcing late reproduction by artificial selection. The fly survival was measured at different time points, as well as two traits that have been proposed to be causally responsible for wMelPop virulence: its relative density and the mean number of copies of octomom, an 8-genes region of the Wolbachia genome. We hypothesised that these conditions (high temperature and late reproduction) would select for a reduced wMelPop virulence, a reduced wMelPop density, and a reduced octomom copy number. Our results indicate that density, octomom copy number and virulence are correlated to each other. However, contrary to our expectations, we could not detect any reduction in virulence during the course of evolution. We discuss the significance of our results with respect to the evolutionary causes of wMelPop virulence.

Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes ofCotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp,Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.

Symbiosis is a continuum of long-term interactions ranging from mutualism to parasitism, according to the balance between costs and benefits for the protagonists. The density of endosymbionts is, in both cases, a key factor that determines both the transmission of symbionts and the host extended phenotype, and is thus tightly regulated within hosts. However, the evolutionary and molecular mechanisms underlying bacterial density regulation are currently poorly understood. In this context, the symbiosis between the fruit fly and its intracellular bacteria Wolbachia ( w MelPop strain) is particularly interesting to study. Although vertically transmitted, the symbiont is pathogenic, and a positive correlation between virulence and w MelPop density is observed. In addition, the number of repeats of a bacterial genomic region -Octomom-is positively correlated with Wolbachia density, underlying a potential genetic mechanism that controls bacterial density. Interestingly, the number of repeats varies between host individuals, but most likely also within them. Such genetic heterogeneity within the host could promote conflicts between bacteria themselves and with the host, notably by increasing within-host competition between symbiont genotypes through a process analogous to the tragedy of the commons. To characterize the determinisms at play in the regulation of bacterial density, we first introgressed wMelPop in different genetic backgrounds of D. melanogaster , and found different density levels and Octomom copy numbers in each host lineage. To determine whether such variations reflect a host genetic determinism on density regulation through Octomom copy number selection, we replicated the introgressions and performed reciprocal crosses on the two Drosophila populations with the most extreme density levels. In both experiments, we detected an absence of directionality in the patterns of infection, associated with a strong instability of these patterns across generations. Given that bacterial density was highly correlated with Octomom copy numbers in all experiments, these results rather suggest a strong influence of drift and a random increase in the frequency of certain bacterial variants. We then discuss how drift, both on the symbiont population during transmission and on the host population, could limit the efficiency of selection in such a symbiotic system, and the consequences of drift on the regulation of density and composition of bacterial populations.

An increasing number of organisms are subjected to abiotic (e.g., air, water, and soil quality, temperature), but also biotic (e.g., new pathogens) stressors. These stressors may disturb the chemical and physiological homeostasis of living systems, and thus impact their ecology and evolution. Because eukaryotes are often associated with symbionts, these changes do not only impact the host but rather the holobiont, an assemblage of interacting species. Indeed, stressors can modify the symbiotic community composition and functions directly, but also indirectly through their impact on host physiology. Any disruption of the symbiotic homeostasis can then impact the host fitness. On the other side, several symbionts protect their host against various threats, and they may facilitate the adaptation of the holobiont to the new environment by limiting the negative impact of stress on the host. It now remains to clarify if their presence constitutes a driver of adaptation of the host or an obstacle limiting the selection of adaptive traits in the host, and to discuss if symbiosis is always the optimal strategy to cope with stressors. The reciprocal impact between stress and symbiosis can become more complex when stressors are considered in combination, as it occurs in nature. Indeed, synergistic or antagonistic effects may impact the holobiont response, and studies characterizing individual disturbances may not be sufficient. In the current context of climate change and globalized pollution, it is thus crucial to develop integrative approaches to predict how organisms, communities and ecosystems will face combinations of stressors.