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 30-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 30-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.