Abstract
RNA silencing is an important innate antiviral defense in plants. Soil-borne plant viruses naturally infect roots via soil-inhabiting vectors, but it is unclear how antiviral RNA silencing responds to virus infection in this particular tissue. In this study, viral small interfering RNA (siRNA) profiles from leaves and roots of wheat plants naturally infected with a soil-borne virus, wheat yellow mosaic virus (WYMV, genus Bymovirus), were analyzed by deep sequencing. WYMV siRNAs were much more abundant in roots than leaves, which was positively correlated with the accumulation of viral RNA. WYMV siRNAs in leaves and roots were predominantly 21- and 22-nt long and equally derived from the positive- and negative-strands of the viral genome. WYMV siRNAs from leaves and roots differed in distribution pattern along the viral genome. Interestingly, compared to siRNAs from leaves (and most other reports), those from roots obviously had a lower A/U bias at the 5′-terminal nucleotide. Moreover, the expression of Dicer-like genes upon WYMV infection were differently regulated between leaves and roots. Our data suggest that RNA silencing in roots may operate differently than in leaves against soil-borne virus invasion.
Highlights
Virus infection in plants is usually associated with the accumulation of virus-derived small interfering RNAs that play essential roles in antiviral RNA silencing defense by degrading viral RNA in a sequence-specific manner (Llave, 2010; Zhang et al, 2015; Li M.L. et al, 2016)
Our RT-qPCR showed that accumulation of WYMV was about 30fold higher in roots than in leaves (Figure 1A), which was positively correlated with the accumulation of virus-derived small interfering RNAs (vsiRNAs)
This result suggests that the high levels of viral replication might provide more double-stranded RNA (dsRNA) substrates for the generation of vsiRNAs in roots by the host RNA silencing machinery
Summary
Virus infection in plants is usually associated with the accumulation of virus-derived small interfering RNAs (vsiRNAs) that play essential roles in antiviral RNA silencing defense by degrading viral RNA in a sequence-specific manner (Llave, 2010; Zhang et al, 2015; Li M.L. et al, 2016). Recent comparative studies of siRNAs of the same virus in different host plants (genotypes), or siRNAs of different viruses (strains) in the same host plant, have provided deeper insights into the link between viral pathogenicity and vsiRNA profiles (Naveed et al, 2014; Margaria et al, 2015, 2016; Ogwok et al, 2016). In our recent study of cucumber green mottle mosaic virus (genus Tobamovirus) siRNAs from leaves and fruits, vsiRNAs in leaves were predominantly derived from the viral positive-strand RNA, whereas those in fruits were derived from both strands, suggesting that the biogenesis of vsiRNAs might differ in the different tissues (Li J. et al, 2016)
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