Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation

Abstract

BackgroundVirus-derived siRNAs (vsiRNAs)-mediated RNA silencing plays important roles in interaction between plant viruses and their hosts. Southern rice black-streaked dwarf virus (SRBSDV) is a newly emerged devastating rice reovirus with ten dsRNA genomic segments. The characteristics of SRBSDV-derived siRNAs and their biological implications in SRBSDV-rice interaction remain unexplored.MethodsVsiRNAs profiling from SRBSDV-infected rice samples was done via small RNA deep sequencing. The putative rice targets of abundantly expressed vsiRNAs were bioinformatically predicted and subjected to functional annotation. Differential expression analysis of rice targets and RNA silencing components between infected and healthy samples was done using RT-qPCR.ResultsThe vsiRNA was barely detectable at 14 days post infection (dpi) but abundantly present along with elevated expression level of the viral genome at 28 dpi. From the 28-dpi sample, 70,878 reads of 18 ~ 30-nt vsiRNAs were recognized (which mostly were 21-nt and 22-nt), covering 75 ~ 91% of the length of the ten genomic segments respectively. 86% of the vsiRNAs had a <50% GC content and 79% of them were 5’-uridylated or adenylated. The production of vsiRNAs had no strand polarity but varied among segment origins. Each segment had a few hotspot regions where vsiRNAs of high abundance were produced. 151 most abundant vsiRNAs were predicted to target 844 rice genes, including several types of host resistance or pathogenesis related genes encoding F-box/LRR proteins, receptor-like protein kinases, universal stress proteins, tobamovirus multiplication proteins, and RNA silencing components OsDCL2a and OsAGO17 respectively, some of which showed down regulation in infected plants in RT-qPCR. GO and KEGG classification showed that a majority of the predicted targets were related to cell parts and cellular processes and involved in carbohydrate metabolism, translation, and signal transduction. The silencing component genes OsDCL2a, OsDCL2b, OsDCL4, and OsAGO18 were down regulated, while OsAGO1d, OsAGO2, OsRDR1 and OsRDR6 were up regulated, significantly, upon SRBSDV infection.ConclusionsSRBSDV can regulate the expression of rice RNA silencing pathway components and the virus might compromise host defense and influence host pathogenesis via siRNA pathways.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0699-3) contains supplementary material, which is available to authorized users.

siRNAs Derived from Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus Down-modulated the Expression Levels of Endogenous Genes in Phalaenopsis equestris

“…Consistent with previous report for diverse plant-virus-specific sRNAs (Donaire et al, 2008; Lan et al, 2018b; Xu and Zhou, 2017), CymMV and ORSV siRNAs also demonstrated a clear tendency to begin with uracil (U), adenine (A), as compared with cytosine (C) and guanidine (G) (Fig. 2E and F).…”

“…USPs can increase adversity tolerance of plants (Sinha et al, 2016). Besides, our results revealed that 4 target genes (DCL1, argonaute16, RdRP-SHL2, and piRNA biogenesis protein EXD1) were annotated as core components of RNAi response (Table 2), suggesting RNAi response may be targeted and its expression levels be further suppressed by vsiRNAs generated in P. equestris infected with CymMV and ORSV, which is similar to other host-pathogen systems (Xu and Zhou, 2017). Many intracellular pathogens, including viruses, parasites, and bacteria, invade, replicate, spread within and exit their host cells in a cytoskeleton-dependent manner (Gouin et al, 2005; Greber and Way, 2006; Gruenheid and Finlay, 2003).…”

“…In virus-infected sample, the majority (72% and 66%) of siRNAs derived from CymMV and ORSV were 18–22 nt in length, with 21 and 22-nt being most abundant (Fig. 2B and C); however, the majority of siRNAs in many virus-plant systems were 21–24 nt in length, with 21- and 22-nt being also most abundant (Kreuze et al, 2009; Lan et al, 2018b; Li et al, 2016; Mitter et al, 2013; Xu and Zhou, 2017; Yan et al, 2010; Yang et al, 2014). Thus, these results implicated that the homologues of DCL4 and DCL2 in P. equestris may be the predominant DCLs involved in the biogenesis of viral small interfering RNAs (vsiRNAs) which functions as the predominant antiviral silencing mediators (Blevins et al, 2006; Deleris et al, 2006; Ding, 2010; Donaire et al, 2008; Liu et al, 2018; Niu et al, 2017); as for other DCLs of P. equestris participating in vsiRNAs generation will be the future discussed topic.…”

“…6). In other pathogen host systems, viral siRNAs also were shown to target and down modulate the expression levels of its corresponding target genes in host (Lan et al, 2018b; Xu et al, 2017). Thus, these results suggested the potential roles of viral siRNAs in modulating growth and development of host.…”

Barley Yellow Dwarf Virus-GAV-derived vsiRNAs Involved in the Production of Wheat Leaf Yellowing Symptoms by Targeting Chlorophyll Synthase

“…Among which, DCL4-dependent 21-nt vsiRNAs play a dominant role in positive-sense RNA virus-infected plants, whereas DCL2-dependent 22-nt vsiRNAs, can substitute for DCL4 when the expression of DCL4 is inhibited [53,56]. VsiRNAs pro ling of Southern rice black-streaked dwarf virus (SRBSDV)-infected rice plants showed that 21-and 22-nt were the most abundant vsiRNAs, supposed that DCL4 and DCL2 are the primary RNA silencing component for generating vsiRNAs [57]. The vsiRNAs obtained from Rice black-streaked dwarf virus (RBSDV) infected maize and rice plants accumulated preferentially as 21-and 22-nt [58,59].…”