Monday, January 30, 2023 - Thesis defense - Deborah Schönegger

Deborah Schönegger

Team Virology

Monday, January 30, 2023 - 2:30 p.m. - Amphithéâtre Colette & Josy Bové - Campus INRAE Villenave d'Ornon

Abstract : HTS-based metagenomics has revolutionized our view of biodiversity and has become a powerful tool in plant virus diagnostics and ecology, allowing to theoretically capture without prior knowledge all viruses present in a sample. However, as with any technology, HTS strategies and the corresponding data processing pipelines need to be validated to provide reliable assessments of plant health status and balance the cost of sequencing with the specificity and sensitivity levels required by the study. In this context, metagenomics benchmarking efforts are often based on mock communities of known composition thus allowing to compare the actual vs the expected performance. Despite their importance, such comparative studies in virology are mainly limited to the clinical sector and are largely lacking in the plant virology field. In the present thesis both methodological challenges and ecological questions in relation to the description and analysis of plant virus communities have been addressed. Phytovirus synthetic communities of varying complexity were used to benchmark the two most frequently used virus enrichment strategies for plant virus metagenomics, virion associated nucleic acids (VANA) and double stranded (ds)RNA. The results show that the dsRNA approach systemically provided a more complete description of the RNA virome but, as expected, performed poorly for DNA viruses. A robust correlation between sample sequencing depth and the completeness of virome description was observed, together with the influence of other parameters such as virome complexity, use of de novo assembled contigs and minimal contig length. In a second more ecologically oriented approach the virome of 45 different wild (Daucus carota ssp. carota) and cultivated carrot (Daucus carota ssp. sativus) populations in France and six additional populations in Spain was analyzed using a dsRNA-based HTS approach. The datasets generated have revealed two important findings: (i) carrots exhibit a particularly diverse virome, rich in novel viruses that were then molecularly characterized and (ii) virus communities differ remarkably between wild and cultivated carrots. The contrasting virome fingerprints between field and wild carrot populations involve both differential presence of some viruses and differential prevalence of other viruses. Based on analysis of individual plants by HTS sequencing and RT-PCR, population genetics of aphid-transmitted viruses were analyzed, highlighting intraspecific viral population differentiation between wild and cultivated hosts for several of them. This is a particularly interesting result considering that both cultivated and wild carrots are members of the same species, and thus represent a pathosystem with expected least genetic and botanical constraints on potential virus flow between a crop and its weedy relative. Taken together, the results obtained suggest a major impact of growth conditions created by agriculture in shaping virome richness and composition. They demonstrated the existence of viral fluxes between the wild and cultivated compartments but also the existence of barriers limiting or altogether preventing exchange of some viruses or of some groups of isolates. The carrot pathosystem used here allowed to gain deep insights into the contrasted viromes that can assemble in closely related plants a the agroecological interface and to provide a baseline for further investigations of the biological and ecological barriers to virus movements and on the complex interaction linking aphid-transmitted viruses in a complex network of mutual interdependencies.

Jury :
M. BOONHAM, Neil - Professeur de University of Newcastle, UK, rapporteur
Mme BRAULT, Véronique - Directrice de recherche INRAE, Strasbourg, rapportrice
Mme. LAINE, Anna-Lisa - Professeur de l’Université de Zurich, Switzerland, Examinatrice
Mme OLIGASTRO, Myléne - Directrice de Recherche INRAE, Montpellier, Examinatrice
M. CANDRESSE, Thierry - Directeur de Recherche INRAE, Bordeaux, Directeur de thèse