Sohini Claverie defended her thesis on 2 June 2020. Carried out within the framework of the E-Space flagship project and funded by Agropolis Fondation, her subject was "Study of the diversity and structure of viral comunities at the scale of agro-ecosystems. The epidemiological model of Poaceae mastreviruses in La Reunion".
Sohini was supervised by Jean-Michel Lett and hosted within the Sciences, Technologies and Health doctoral school (Saint-Denis, Réunion), in partnership with Peuplements végétaux et bioagresseurs en milieu tropical (Saint-Pierre, Réunion) (laboratory).
Viruses’ ubiquity, abundance and diversity have highlighted that they are naturally embedded into global ecosystems. In order to better understand how they interact, adapt and evolve, it is essential to study them at the ecosystem scale, particularly at the agro-ecosystem scale where the promiscuity between wild and cultivated ecosystems facilitates new interactions favouring the emergence of new viral variants. This study focused on phytoviruses of the genus Mastrevirus, transmitted by leafhoppers and responsible for many crop diseases in Africa and the Indian Ocean islands. Our work focused on the development of a metagenomic approach called RCA-RA-NGS targeting viruses with small circular DNA genomes. This approach is based on rolling-circle amplification step followed with amplicons tagging using random PCR allowing multiplexing of up to 1200 samples and Illumina high-throughput sequencing before classification of the reads obtained by similarity search and phylogenetic placement. The analysis of nearly 3000 samples representing 30 species of Poaceae showed that 18 of these species and globally 8% of the evaluated plants were infected by masteviruses. In addition to the discovery of previously undescribed mastrevirus species, our results provide a comprehensive view of the network of mastrevirus-host association within an agro-ecosystem. The topology of this network suggests (1) no modularity and only nestedness of specialists host ranges with those of generalists, (2) hosts acting as viral hub and (3) the presence of recombination.