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Scanning the virome of Prunus : Identification and characterization of novel luteoviruses and Secoviridae members

M. Khalili. Thèse de doctorat en Science de la Vie et de la Santé, Mention Biologie Végétale, sous la direction de Armelle Marais, Université de Bordeaux, 2022, 178 p. The main objective of this thesis was to explore using advanced sequencing technology the composition of the virome (all the viruses present) of Prunus species (apricot, cherry, peach, plum, almond, and related wild or ornamental species). During this work, beyond known viruses, six novel viruses were discovered, significantly increasing the number of viruses known to infect Prunus. Diagnostic tests have been developed, allowing to detect them specifically. We have shown that some of the peach-infecting viruses have a very wide distribution in Europe, without causing any apparent symptoms. Overall, this exploration of the Prunus virome has enriched our knowledge of these viruses and provided new elements to assess the risks associated with these different agents. They open new research perspectives to account for their potential impact.

The main objective of this thesis was to determine the composition of the virome of several Prunus species in order to identify known and novel viruses that compose it, to characterize some of them and to develop diagnostic tools, allowing their detection. In order to maximize the genetic diversity within the targeted Prunus species, the virome of 300 accessions from cultivated or related species, gathered in the INRAE Prunus Biological Resource Center (BRC) was analyzed. Thus, accessions of Prunus armeniaca (apricot), P. persica (peach), P. domestica (plum), P. avium (sweet cherry), P. cerasus (sour cherry), and related species were subjected to HTS indexing. Wild or ornamental Prunus collected in other studies were also analyzed. For this purpose, double-stranded RNAs, proxy of viral infection by RNA viruses, were purified and analyzed. In addition to the viruses classically known to infect Prunus species, four new viruses belonging to the genus Luteovirus were identified in various Prunus species: peach, apricot, sour cherry, Japanese apricot (P. mume), an ornamental cherry (P. incisa) or a wild species, P. mahaleb. In addition, a search in the Prunus databases for viral sequences allowed the reconstruction of the genome of another luteovirus potentially infecting a wild species, P. humilis. Prior to this study, only three luteoviruses were known to infect Prunus trees. The identification and characterization of these five new luteoviruses therefore represent an important advance in the knowledge of these agents. A Europe-wide study showed that the three peach-infecting luteoviruses (including one new agent) were widely distributed with high prevalence rates, in agreement with the data obtained in the peach collection of the Prunus BRC. Transmission assays of these three luteoviruses to the biological indicator GF305, as well as observation of infected trees in the BRC, suggest that these viruses most likely do not induce significant symptoms, which would explain why they have gone undetected until now, despite their very wide distribution. In addition, the complete genomic sequence of four viruses of the Secoviridae family was determined during this work, including a new cheravirus identified and characterized in two wild species (P. mahaleb and P. brigantina) and in an apricot accession from the BRC. Efficient RT-PCR detection tests were developed for each of the new viruses studied. Overall, this exploration of the Prunus virome has enriched our knowledge of the viruses infecting this family and has provided new elements to start assessing the potential risks linked to these different agents. These results open new research perspectives to account for their impact. 

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