Abstract
Northern-blot hybridization and low-scale sequencing have revealed that plants infected by viroids, non-protein-coding RNA replicons, accumulate 21–24 nt viroid-derived small RNAs (vd-sRNAs) similar to the small interfering RNAs, the hallmarks of RNA silencing. These results strongly support that viroids are elicitors and targets of the RNA silencing machinery of their hosts. Low-scale sequencing, however, retrieves partial datasets and may lead to biased interpretations. To overcome this restraint we have examined by deep sequencing (Solexa-Illumina) and computational approaches the vd-sRNAs accumulating in GF-305 peach seedlings infected by two molecular variants of Peach latent mosaic viroid (PLMVd) inciting peach calico (albinism) and peach mosaic. Our results show in both samples multiple PLMVd-sRNAs, with prevalent 21-nt (+) and (−) RNAs presenting a biased distribution of their 5′ nucleotide, and adopting a hotspot profile along the genomic (+) and (−) RNAs. Dicer-like 4 and 2 (DCL4 and DCL2, respectively), which act hierarchically in antiviral defense, likely also mediate the genesis of the 21- and 22-nt PLMVd-sRNAs. More specifically, because PLMVd replicates in plastids wherein RNA silencing has not been reported, DCL4 and DCL2 should dice the PLMVd genomic RNAs during their cytoplasmic movement or the PLMVd-dsRNAs generated by a cytoplasmic RNA-dependent RNA polymerase (RDR), like RDR6, acting in concert with DCL4 processing. Furthermore, given that vd-sRNAs derived from the 12–14-nt insertion containing the pathogenicity determinant of peach calico are underrepresented, it is unlikely that symptoms may result from the accidental targeting of host mRNAs by vd-sRNAs from this determinant guiding the RNA silencing machinery.
Highlights
Viroids are subviral replicons exclusively composed of a small (246–401 nt) circular RNA that, even though lacking proteincoding capacity, is able to infect higher plants and often induce specific diseases [see for reviews 1–5]
We carried out our deep sequencing study starting from two preparations of gel-purified sRNAs from GF-305 peach seedlings infected by peach calico (PC)-C40 and GDS6 variants (Fig. 1)
Peach latent mosaic viroid (PLMVd)-sRNA analysis was simplified because the progenies resulting from the two specific PLMVd variants, which come from greenhouse plants that have been infected for a short time, are considerably less complex populations than those from field trees [26] that may have been infected for a long time
Summary
Viroids are subviral replicons exclusively composed of a small (246–401 nt) circular RNA that, even though lacking proteincoding capacity, is able to infect higher plants and often induce specific diseases [see for reviews 1–5]. Viroids are classified into two families: Pospiviroidae, the members of which replicate in the nucleus through an asymmetric rolling-circle mechanism catalyzed by host enzymes [6,7], and Avsunviroidae, whose members replicate in the chloroplast through a symmetric rolling-circle mechanism involving host enzymes and cis-acting hammerhead ribozymes embedded in the viroid strands of both polarities [8,9] Despite their fundamental differences with viruses in structure, function and evolutionary origin, research on viroids has been deeply influenced by previous discoveries on viruses and, on plant riboviruses. This is the case of pathogenesis —symptoms incited by viruses and viroids are to a good extent similar— suggesting that some steps of the underlying mechanism might be shared by both biological entities. These results raise the question of whether viroids are triggers, targets and even suppressors of the RNA silencing machinery of their hosts
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
