# Comparative small RNA profiles of beet mosaic virus (BtMV), beet mild yellowing virus (BMYV) and beet yellows virus (BYV) infected Nicotiana benthamiana and Beta vulgaris

## TL;DR

This study compares RNA profiles in plants infected with three viruses to identify virus-specific RNA targets for potential non-transgenic virus control methods.

## Contribution

The study identifies virus-specific vsiRNA hotspots that are consistent across host species, offering targets for RNA interference-based sprays.

## Key findings

- vsiRNA profiles differ by virus type but not by host plant species.
- Distinct vsiRNA hotspots were detected for each virus, suggesting potential targets for RNA interference.
- The findings support the use of synthetic dsRNA sprays as a non-transgenic strategy to control viral infections.

## Abstract

•Plants use RNA silencing to restrict viral infection via vsiRNAs.•vsiRNAs of BtMV, BMYV and BYV in sugar beet and tobacco were analysed.•vsiRNA profiles differ by virus type and but not by plant host species.•vsiRNA hotspots identified target regions for dsRNA sprays for virus control.

Plants use RNA silencing to restrict viral infection via vsiRNAs.

vsiRNAs of BtMV, BMYV and BYV in sugar beet and tobacco were analysed.

vsiRNA profiles differ by virus type and but not by plant host species.

vsiRNA hotspots identified target regions for dsRNA sprays for virus control.

Plants are constantly challenged by viral pathogens that can limit growth and reduce yield. A key component of the plant innate immunity is RNA silencing, in which viral double-stranded RNA (dsRNA) intermediates are recognised and processed into virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs direct the degradation of viral genomes, thereby restricting infection. Sugar beet (Beta vulgaris subsp. vulgaris) is a crop of major economic importance, where the virus yellows (VY) complex represents a serious threat to production. Here, we profiled and compared vsiRNAs generated during infection of the natural host plant B. vulgaris and the experimental host plant Nicotiana benthamiana with three taxonomically distinct viruses: beet yellows virus (BYV, Closterovirus), beet mild yellowing virus (BMYV, Polerovirus), and beet mosaic virus (BtMV, Potyvirus). High-throughput sequencing of small RNAs revealed characteristic size distributions and strand biases that differed among viruses and host species. Comparative analysis highlighted no host plant-specific pattern of vsiRNA accumulation. This comparative approach provides a detailed view of vsiRNA processing and offers novel insights that are not apparent from coverage profiles alone. Distinct vsiRNA hotspots were detected for each viral genome, and these hotspots did not differ between host plants, pinpointing potential target regions for RNA interference-based control approaches. The identification of such regions provides a basis for the design of synthetic dsRNAs that can be applied exogenously as protective sprays, an emerging, non-transgenic strategy to mitigate VY infections, while advancing understanding of vsiRNA biogenesis in sugar beet and N. benthamiana in general.

Image, graphical abstract