Rhizomania is a major disease of sugar beet caused by Beet necrotic yellow vein virus (BNYVV), a benyvirus transmitted by the root-infecting
plasmodiophorid protist Polymyxa betae. The obligate parasitic nature of plasmodiophorid organisms has long hampered efforts to obtain axenic
cultures and complicated the sequencing of their entire genome. In this thesis, genomes of two P. betae isolates were, for the first time, assembled from
distinct DNA samples using cutting-edge metagenomic techniques. The two nuclear genomes are very similar, each with ~10.2k protein-coding genes.
Extending genomic comparisons to other plasmodiophorids, including mitochondrial sequences, revealed a greater overlap with Spongospora
subterranea than with Plasmodiophora brassicae. Putative virulence factors found in P. betae are absent from other plasmodiophorids, and vice versa,
revealing that they probably use distinct strategies to invade their hosts. A new protocol for the soil-free transmission of BNYVV to sugar beet by P. betae
zoospores was developed and successfully applied to perform transcriptomic analysis of the tripartite interaction in rhizomania, using genetically
characterized organisms. When nonviruliferous P. betae was inoculated in sugar beet, the protist implemented a strategy to circumvent plant defenses.
The presence of BNYVV accelerated the development of P. betae, probably due to the action of the virus on plant cell walls and/or to its ability to suppress
host RNA silencing. Moreover, BNYVV enhanced the induction of plant defenses and accelerated sporosori production. This earlier transition to the
survival stage could either be due to the stress induced by plant defenses on P. betae or to a lack of resources or free root cells (not already containing
protist structures) for further multiplication of P. betae.
 

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