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Putative new plant viruses associated with Plasmopara viticola-infected grapevine samples

In this study, we analysed a total of 16 libraries from over 150 grapevine leaf and grape samples infected with Plasmopara viticola (downy mildew of grapevine) to characterise the virome associated to this oomycete. Samples were collected in five distinct regions in Italy and in four different regions in Spain, representative of different pedoclimatic conditions and different grapevine cultivars during 2018 growing season. Due to the metagenomics nature of the samples (containing at least both downy mildew hyphae and spores, and grapevine cells residues), we were able to assemble several plant viruses and a few possible novel plant virus genomes with our in silico analysis. We detected several plant virus variants already reported in grapevine, and a putative new ilarvirus previously unreported in grapevine. Furthermore, we characterised three new phenui-like viruses (in the order Bunyavirales), one of which shares some commonalities with plant coguviruses. Finally, we report a new strict association of three viral segments (one flavi-like and two virga-like) that we propose to be a new virus taxon named jivivirus.

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FIGURE. Phylogenetic analysis of a selected number of viral proteins closely related to those expressed by jivivirus RNA1 (helicase, methyltransferase virga-like) (a), RNA2 (putative RdRP virga-like) (b) and RNA3 (flavivirus NS3-like) (c). The máximum likelihood (ML) methodology was used to infer the best tree. The best substitution models were WAG+F + I + G4 (for RNA1 expressed proteins) with a log-likelihood of consensus tree: −24,158.092193; Blosum62 + F + I + G4 (for RNA2 expressed protein) with a log-likelihood of the tree: −35,144.3099; VT (for RNA3 expressed protein) with a log likelihood of the tree: −7,608.1139. Red diamonds indicate the viruses assembled in this work. At nodes the percentage bootstrap values

Original Paper:

Chiapello, M., Rodríguez‐Romero, J., Nerva, L., Forgia, M., Chitarra, W., Ayllón, M.A., Turina, M. 2019. Putative new plant viruses associated with Plasmopara viticola-infected grapevine samples. Annals of Applied Biology. DOI: 10.1111/aab.12563

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