Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses

Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta

Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de virulence qui utilise un symbionte viral de la famille des Polydnavirus nommé Cotesia congregata bracovirus. Mon travail de thèse a permis de caractériser le dialogue moléculaire au cours de l’interaction par des approches de transcriptomique à haut débit et de physiologie. Ces travaux ont permis d’établir la première carte fonctionnelle du génome viral et de visualiser l’ensemble des gènes de M. sexta régulés au cours du parasitisme. La régulation des gènes de l’immunité a révélé que le parasitisme n’empêche pas l’induction de peptides antimicrobiens, mais entraine la sous-expression de gènes impliqués dans la réponse cellulaire. De plus j’ai pu mettre en évidence une réduction du nombre de cellules adhérentes au cours de l’interaction et décrire l’induction d’un phénotype de type apoptose d’une catégorie de cellules immunitaires. Ces résultats permettent d’identifier des gènes acteurs de l’interaction et apportent de nouvelles connaissances relatives aux interactions hôtes-parasitoïdes.Cotesia congregata is a parasitoid wasp that develops inside the lepidopteran larvae, Manduca sexta. This parasitoid wasp has evolved virulence strategies using an obligate viral symbiont from the Polydnavirus family named Cotesia congregata bracovirus. My thesis work has allowed us to characterize the molecular dialogue during the interaction by physiological and high-throughput transcriptomic approaches. This work allowed to obtain the first functional map of the viral genome and to identify all M. sexta genes regulated during parasitism. Regulation of immune genes revealed that parasitism does not prevent induction of antimicrobial peptides, but leads to the down-regulation of genes involved in the cellular response. Moreover, I was able to demonstrate a reduction in the number of adherent cells during the interaction and to describe this induction as an apoptosis-like phenotype targeting a specific population of immune cells. These findings open the way to the identification of candidate genes involved in this particular interaction and provide new insights into host-parasitoid interactions in general

Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta

Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de virulence qui utilise un symbionte viral de la famille des Polydnavirus nommé Cotesia congregata bracovirus. Mon travail de thèse a permis de caractériser le dialogue moléculaire au cours de l’interaction par des approches de transcriptomique à haut débit et de physiologie. Ces travaux ont permis d’établir la première carte fonctionnelle du génome viral et de visualiser l’ensemble des gènes de M. sexta régulés au cours du parasitisme. La régulation des gènes de l’immunité a révélé que le parasitisme n’empêche pas l’induction de peptides antimicrobiens, mais entraine la sous-expression de gènes impliqués dans la réponse cellulaire. De plus j’ai pu mettre en évidence une réduction du nombre de cellules adhérentes au cours de l’interaction et décrire l’induction d’un phénotype de type apoptose d’une catégorie de cellules immunitaires. Ces résultats permettent d’identifier des gènes acteurs de l’interaction et apportent de nouvelles connaissances relatives aux interactions hôtes-parasitoïdes.Cotesia congregata is a parasitoid wasp that develops inside the lepidopteran larvae, Manduca sexta. This parasitoid wasp has evolved virulence strategies using an obligate viral symbiont from the Polydnavirus family named Cotesia congregata bracovirus. My thesis work has allowed us to characterize the molecular dialogue during the interaction by physiological and highthroughput transcriptomic approaches. This work allowed to obtain the first functional map of the viral genome and to identify all M. sexta genes regulated during parasitism. Regulation of immune genes revealed that parasitism does not prevent induction of antimicrobial peptides, but leads to the downregulation of genes involved in the cellular response. Moreover, I was able to demonstrate a reduction in the number of adherent cells during the interaction and to describe this induction as an apoptosis-like phenotype targeting a specific population of immune cells. These findings open the way to the identification of candidate genes involved in this particular interaction and provide new insights into host-parasitoid interactions in general

De novo transcriptome assembly and analysis of the Flat Oyster pathogenic protozoa Bonamia ostreae

Here are the supplementary materials related to the study entitled "De novo transcriptome assembly and analysis of the Flat Oyster pathogenic protozoa Bonamia ostreae".Raw sequencing data are available under accession PRJNA731671 at NCBI.</div

De novo transcriptome assembly and analysis of the Flat Oyster pathogenic protozoa Bonamia ostreae

Here are the intermediate files related to variant calling of the B. ostreae rRNA operon

Herpesviruses: overview of systematics, genomic complexity and life cycle

Herpesviruses are double-stranded DNA viruses with distinct morphological features and are among the largest and most complex viruses. According to the International Committee on Taxonomy of Viruses (ICTV), in 2022, there were 133 herpesviruses classified into three families: Orthoherpesviridae, infecting mammals and birds; Malacoherpesviridae infecting marine molluscs; and Alloherpesviridae infecting fish and amphibians. Herpesviruses have a complex genomic architecture, characterised by unique regions flanked by repeated and inverted sequences. Unique regions can undergo rearrangements leading to the formation of genomic isomers, which could have important implications for the life cycle of the virus. Herpesviruses life cycle consists of two main phases: the lytic phase, during which viral genes are expressed and translated into viral proteins that regulate DNA replication, capsid formation and the production of new particles; and the persistence phase, in which the virus persists in the host without being eliminated by the immune system. This review offers an updated and comprehensive overview of the Herpesvirales order, detailing their morphological characteristics, providing an in-depth taxonomic classification, examining their genomic architecture and isomers, and describing their life cycle

Origin and evolution of symbiotic viruses associated with parasitoid wasps

National audienceThe Polydnaviridae (PDV), including the Bracovirus (BV) and Ichnovirus (IV) genera, originated from the integration of viruses in the genomes of two parasitoid wasp lineages. In a remarkable example of convergent evolution BVs evolved from the domestication of a nudivirus, while IVs originate from a different ancestral virus belonging to a new virus entity. In both cases the ancestor genomes have been maintained in wasp genomes as endogenous viral elements involved in production of particles containing DNA encoding virulence genes that are injected into lepidopteran hosts. However many PDV virulence genes appear to be of eukaryotic origin, and expansion and diversification of these genes have led to the production of novel PDVs in different wasp species that promote survival of offspring in particular hosts

De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae

The flat oyster Ostrea edulis is an oyster species native to Europe. It has declined to functional extinction in many areas of the NE Atlantic for several decades. Factors explaining this decline include over-exploitation of natural populations and diseases like bonamiosis, regulated across both the EU and the wider world and caused by the intracellular protozoan parasite Bonamia ostreae. To date, very limited sequence data are available for this Haplosporidian species. We present here the first transcriptome of B. ostreae. As this protozoan is not yet culturable, it remains extremely challenging to obtain high-quality -omic data. Thanks to a specific parasite isolation protocol and a dedicated bioinformatic pipeline, we were able to obtain a high-quality transcriptome for an intracellular marine micro-eukaryote, which will be very helpful to better understand its biology and to consider the development of new relevant diagnostic tools