Wednesday, October 26, 2022 - Thesis defense - Maryam KHALILI

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


Team Plant Virology

Wednesday, October 26, 2022 - 2:00 p.m. - Amphithéâtre Colette & Josy Bové - Campus INRAE Villenave d'Ornon

Maryam Khalili

Abstract : Major advances in biology have often been linked to important technological innovations. High-Throughput Sequencing (HTS) technologies are undoubtedly one of the most important inventions of recent years, having a major impact on the discovery of new viruses. HTS allows to characterize without a priori the virome of a sample, i.e. all the viruses present. Nevertheless, the advent of HTS was only possible thanks to the concomitant progress of bioinformatics tools allowing to exploit massive sequencing data. The present thesis was carried out in the framework of a Marie-Curie training network named « INEXTVIR - Innovative Network for Next Generation Training and Sequencing of Virome » which aims to better understand viral communities and their role in agricultural ecosystems, using the latest advances in HTS. 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, Prunus 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.

Jury :


Professeure, NIB, Slovénie


M. JELKMANN, Wilhelm

Professeur, JKI, Allemagne


M. LEMAIRE, Olivier

Directeur de Recherche,INRAE, Colmar


Mme FORGET, Florence

Directrice de Recherche, INRAE, Bordeaux


M. GENTIT, Pascal

Ingénieur de Recherche, ANSES, Angers


Mme MARAIS Armelle

Ingénieure de Recherche, INRAE, Bordeaux

Directrice de thèse

Modification date : 17 October 2023 | Publication date : 03 October 2022 | Redactor : M. Gauthier