Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Ligustrum vulgare) in Europe

• Published in: Frontiers in microbiology Vol. 12; p. 723350
• Main Authors: Reynard, Jean-Sébastien, Turco, Silvia, Brodard, Justine, Kellenberger, Isabelle, Maclot, François, Schumpp, Olivier, Gugerli, Paul, Pooggin, Mikhail M.
• Format: Journal Article Web Resource
• Language: English
• Published: Frontiers Media 27.09.2021; Frontiers Media S.A
• Subjects: Biologie végétale (sciences végétales, sylviculture, mycologie...); distribution; Environmental sciences & ecology; genome; Hordeivirus; Life Sciences; Ligustrum; Microbiology; Microbiology (medical); phylogeny; Phytobiology (plant sciences, forestry, mycology...); Phytopathology and phytopharmacy; Sciences de l’environnement & écologie; Sciences du vivant; siRNAs; transmission; Vegetal Biology; virions; genome; transmission; phylogeny; Hordeivirus; distribution; Ligustrum; virions; siRNAs
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.723350

Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub Ligustrum vulgare (privet) was recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and de novo assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3′-terminal common region (CR) attached to each segment via a ∼53–71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus Hordeivirus of family Virgaviridae , which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts Chenopodium quinoa and Nicotiana benthamiana . Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3′-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.