Identification of virus‐derived siRNAs and their targets in RBSDV‐infected rice by deep sequencing

Abstract

RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies. Through deep sequencing, genome-wide comparisons of RBSDV-derived vsiRNAs were made between the japonica variety Nipponbare, and the indica variety 9311. Four small RNA libraries were constructed from the leaves and shoots of each variety. We found 659,756 unique vsiRNAs in the four samples, and only 43,485 reads were commonly shared. The size distributions of vsiRNAs were mostly 21- and 22-nt long, and A/U bias (66-68%) existed at the first nucleotide of vsiRNAs. Additionally, vsiRNAs were continuously but heterogeneously distributed along S1-S10 segments of the RBSDV genome. Distribution profiles of vsiRNA hotspots were similar in different hosts and tissues, and the 5'- and 3'-terminal regions of S4, S5, and S8 had more hotspots. Distribution and abundance of RBSDV vsiRNAs could be useful in designing efficient targets for exploiting RNA interference for virus resistance. Degradome analysis found 25 and 11 host genes appeared to be targeted by vsiRNAs in 9311 and Nipponbare. We report for the first time vsiRNAs derived from RBSDV-infected rice.

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).…”

“…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.…”

“…2G and H). This is broadly contrasted to many single-stranded RNA (ssRNA) positive-strand viruses, siRNAs of which were produced equally from the positive and the negative strands or predominantly from negative strands of viral genomes (Ho et al, 2007; Lan et al, 2018b; Li et al, 2016; Xia et al, 2014; Yang et al, 2014). Furthermore, single-base resolution maps of total CymMV and ORSV siRNAs along with genomes were created using Bowtie tools and in-house Perl scripts.…”

“…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.…”

Nitric Oxide Enhances Rice Resistance to Rice Black-Streaked Dwarf Virus Infection

“…Rice cv. Nipponbare is known to be susceptible to RBSDV infection (Lan et al 2018), and rice cv. 15HPO187 was found to be resistant to RBSDV infection in our earlier field surveys.…”