The genetic diversity of three temperate fruit tree phytoplasmas ‘Candidatus Phytoplasma prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ has been established by multilocus sequence analysis. Among the four genetic loci used, the genes imp and aceF distinguished 30 and 24 genotypes, respectively, and showed the highest variability. Percentage of substitution for imp ranged from 50 to 68 % according to species. Percentage of substitution varied between 9 and 12 % for aceF, whereas it was between 5 and 6 % for pnp and secY. In the case of ‘Ca P. prunorum’ the three most prevalent aceF genotypes were detected in both plants and insect vectors, confirming that the prevalent isolates are propagated by insects. The four isolates known to be hypo-virulent had the same aceF sequence, indicating a possible monophyletic origin. Haplotype network reconstructed by eBURST revealed that among the 34 haplotypes of ‘Ca. P. prunorum’, the four hypo-virulent isolates also grouped together in the same clade. Genotyping of some Spanish and Azerbaijanese ‘Ca. P. pyri’ isolates showed that they shared some alleles with ‘Ca. P. prunorum’, supporting for the first time to our knowledge, the existence of inter-species recombination between these two species.

Understanding at which spatiotemporal scale a disease causes significant secondary spread has both theoretical and practical implications. We investigated this issue in the case of European stone fruit yellows (ESFY), a quarantine vector-borne phytoplasma disease of Prunus trees. Our work was focused on the processes underlying disease spread: the interplay between the life cycles of the pathogen (‘Candidatus Phytoplasma prunorum’) and of the vector (Cacopsylla pruni). We demonstrated experimentally that C. pruni has only one generation per year and we showed that, at least in southeastern France, C. pruni migrates between conifers in mountainous regions (where it overwinters) and Prunus spp. at lower altitude (where it breeds). In acquisition–inoculation experiments performed with C. pruni over its period of presence on Prunus spp., both immature and mature C. pruni were hardly infectious (0.6%) despite effective phytoplasma acquisition and multiplication. We demonstrated that most immature vectors born on infected plants reach their maximum phytoplasma load (10⁷genomes per insect) only after migrating to conifers and that, after a life-long retention of the phytoplasma, their transmission efficiency was very high (60%) at the end of winter (when they migrate back to their Prunus host). Thus, most transmissions occur only after an effective latency of 8 months, following vector migrations and overwintering on conifers in mountainous regions. From this transmission cycle, we can infer that local secondary spread of ESFY in apricot orchards is marginal, and recommend that disease management strategies take more into account the processes occurring at a regional scale, including the role of wild Prunus spp. in ESFY epidemics.