Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Abstract

RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.

Badnaviruses of Sweet Potato: Symptomless Coinhabitants on a Global Scale

“…In addition, the size distribution of siRNAs mapped to the SPPV genomes showed that the relative abundance of 22-nt siRNAs was higher than that of 24-nt siRNAs ( Figure 5B). EPRVs usually spawn predominantly 24-nt siRNA (Pooggin, 2018). The abundance of 22-nt siRNAs is consistent with episomal replication.…”

“…We noted that siRNA mapping to the viral genomes revealed a ∼300-bp region in the SPPV-A (but not SPPV-B) genome (Figure 5A), where no siRNAs mapped. This has not been observed for other Badnavirus sequenced by siRNA ( (Pooggin, 2018) and references therein). This region was sequenced from several PCR fragments with ample overlap to flanking regions, which were targeted by siRNAs, and we currently have no explanation for this observation.…”

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

“…target Endogenous Viral Elements, virus segments that are integrated in the host genome, that 550 form inverted repeats (Pooggin 2018). To understand the role of the siRNA22 loci, the next step 551…”

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

“…Both DNA and RNA viruses can be detected by sequencing of small RNAs generated by RNA silencing during plant defence [36][37][38]. However, presence of small endogenous plant RNAs can interfere with viral genome assembly and coverage of the viral genome can be uneven when sequenced from small RNAs [39,40].…”