Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle Mosaic Virus-Infected Lagenaria siceraria Plants

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.

Differential Characteristics of Viral siRNAs between Leaves and Roots of Wheat Plants Naturally Infected with Wheat Yellow Mosaic Virus, a Soil-Borne Virus

“…Nevertheless, most studies of vsiRNA profiles in plants have used infected leaf tissue, and there is little evidence from other tissues. 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 equally from both strands, suggesting that the biogenesis of vsiRNAs might differ in the different tissues ( Li J. et al, 2016 ).…”

Transcriptome analysis of watermelon (Citrullus lanatus) fruits in response to Cucumber green mottle mosaic virus (CGMMV) infection

“…Several virus-plant interaction analyses have been performed at the transcriptional level to study both the physiological and metabolic processes variations of infected plants 21 – 23 . Virus-derived small interfering RNAs (vsiRNAs) profiles of CGMMV-infected cucumber 24 and different tissues from bottle gourd 25 have been investigated via high-throughput sequencing, and the results indicated that the characteristics of the vsiRNAs between different host plants or tissues were distinctly different. Eight novel and 23 known miRNAs have been identified that cucumber leaves produced in response to CGMMV infection, which is useful to help elucidate host-pathogen interactions as well as to screen for cucumber resistance genes 6 .…”

Suppression of nbe‐miR166h‐p5 attenuates leaf yellowing symptoms of potato virus X on Nicotiana benthamiana and reduces virus accumulation

“…The read numbers of small RNAs were normalized to ‘reads per million’ (RPM) based on the total small RNA read numbers. The mapping of virus‐derived siRNAs to the combined virus genome sequence was carried out according to the method described previously (Li et al ., ).…”