Abstract
RNA silencing is an evolutionarily conserved antiviral mechanism, through which virus-derived small interfering RNAs (vsiRNAs) playing roles in host antiviral defense are produced in virus-infected plant. Deep sequencing technology has revolutionized the study on the interaction between virus and plant host through the analysis of vsiRNAs profile. However, comparison of vsiRNA profiles in different tissues from a same host plant has been rarely reported. In this study, the profiles of vsiRNAs from leaves and fruits of Lagenaria siceraria plants infected with Cucumber green mottle mosaic virus (CGMMV) were comprehensively characterized and compared. Many more vsiRNAs were present in infected leaves than in fruits. vsiRNAs from both leaves and fruits were mostly 21- and 22-nt in size as previously described in other virus-infected plants. Interestingly, vsiRNAs were predominantly produced from the viral positive strand RNAs in infected leaves, whereas in infected fruits they were derived equally from the positive and negative strands. Many leaf-specific positive vsiRNAs with lengths of 21-nt (2058) or 22-nt (3996) were identified but only six (21-nt) and one (22-nt) positive vsiRNAs were found to be specific to fruits. vsiRNAs hotspots were only present in the 5′-terminal and 3′-terminal of viral positive strand in fruits, while multiple hotspots were identified in leaves. Differences in GC content and 5′-terminal nucleotide of vsiRNAs were also observed in the two organs. To our knowledge, this provides the first high-resolution comparison of vsiRNA profiles between different tissues of the same host plant.
Highlights
RNA silencing is a natural antiviral mechanism in plants and other eukaryotic organisms
It has recently been shown that the eukaryotic translation initiation factor 4A of Nicotiana benthamiana can be targeted by siRNA derived from Rice stripe virus (RSV), resulting in leaf-twisting and stunting (Shi et al, 2016). These results indicate the complicated function of virus-derived small interfering RNAs (vsiRNAs) during virus-host interaction
The present study reports markedly different vsiRNA profiles between infected fruits and leaves of Lagenaria siceraria
Summary
RNA silencing is a natural antiviral mechanism in plants and other eukaryotic organisms. DCL4 mainly targets virus RNA to produce 21 nucleotide (nt) vsiRNAs, while DCL2 is responsible for the processing of 22-nt vsiRNAs when DCL4 is absent or its activity is inhibited (Xie et al, 2004; Deleris et al, 2006). DCL1 is mainly responsible for excising the stem-loop structures of primary microRNAs (miRNAs) into mature approximately 21-nt miRNAs that play key roles in post-transcriptional gene silencing (Blevins et al, 2006; Dong et al, 2008). The functions of these DCLs are overlapping and can be complemented. Very low levels of 21-nt vsiRNAs were produced by DCL1 in dcl2/dcl3/dcl triple mutant plants infected with Cucumber mosaic virus (CMV), while 24-nt vsiRNAs were produced by DCL3 in dcl2/dcl double mutant plants, indicating a compensatory role for these DCLs (Bouché et al, 2006; Deleris et al, 2006)
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