RNAseq Analysis of Rhizomania-Infected Sugar Beet Provides the First Genome Sequence of Beet Necrotic Yellow Vein Virus from the USA and Identifies a Novel Alphanecrovirus and Putative Satellite Viruses.

John J Weiland,Roshan Sharma Poudel,Gary A Secor,Melvin D Bolton,Alyssa Flobinus,David E Cook

doi:10.3390/v12060626

Abstract

“Rhizomania” of sugar beet is a soilborne disease complex comprised of beet necrotic yellow vein virus (BNYVV) and its plasmodiophorid vector, Polymyxa betae. Although BNYVV is considered the causal agent of rhizomania, additional viruses frequently accompany BNYVV in diseased roots. In an effort to better understand the virus cohort present in sugar beet roots exhibiting rhizomania disease symptoms, five independent RNA samples prepared from diseased beet seedlings reared in a greenhouse or from field-grown adult sugar beet plants and enriched for virus particles were subjected to RNAseq. In all but a healthy control sample, the technique was successful at identifying BNYVV and provided sequence reads of sufficient quantity and overlap to assemble > 98% of the published genome of the virus. Utilizing the derived consensus sequence of BNYVV, infectious RNA was produced from cDNA clones of RNAs 1 and 2. The approach also enabled the detection of beet soilborne mosaic virus (BSBMV), beet soilborne virus (BSBV), beet black scorch virus (BBSV), and beet virus Q (BVQ), with near-complete genome assembly afforded to BSBMV and BBSV. In one field sample, a novel virus sequence of 3682 nt was assembled with significant sequence similarity and open reading frame (ORF) organization to members within the subgenus Alphanecrovirus (genus Necrovirus; family Tombusviridae). Construction of a DNA clone based on this sequence led to the production of the novel RNA genome in vitro that was capable of inducing local lesion formation on leaves of Chenopodium quinoa. Additionally, two previously unreported satellite viruses were revealed in the study; one possessing weak similarity to satellite maize white line mosaic virus and a second possessing moderate similarity to satellite tobacco necrosis virus C. Taken together, the approach provides an efficient pipeline to characterize variation in the BNYVV genome and to document the presence of other viruses potentially associated with disease severity or the ability to overcome resistance genes used for sugar beet rhizomania disease management.

Highlights

The increasing globalization of food and other commodities has resulted in greater exposure of crops to historical and emerging pests and diseases, including viruses [1,2]
The viruses beet necrotic yellow vein virus (BNYVV), beet soilborne mosaic virus (BSBMV) [29], and beet black scorch virus (BBSV) [28] are known to produce disease symptoms on infected sugar beet plants, whereas plants infected by beet soilborne virus (BSBV) [30] and beet virus Q (BVQ) [31]
The viruses BNYVV, BSBMV [29], and BBSV [28] are known to produce disease symptoms on infected sugar beet plants, whereas plants infected by BSBV [30] and BVQ [31] are relatively asymptomatic

Summary

Introduction

The increasing globalization of food and other commodities has resulted in greater exposure of crops to historical and emerging pests and diseases, including viruses [1,2]. Novel pathogen variants acting alone or in combination may arise to compromise existing resistance in the crop [3,4,5]. Because of the unanticipated complexities wrought by such phenomena in disease development and crop protection, accurate, rapid and, increasingly, naïve diagnostics and analyses are required to keep pace with the accelerating diversity in pests and pathogens. “Rhizomania” is considered to be the most devastating root disease of sugar beet globally and is managed principally through genetic resistance in the host [7,8].

Methods

Results

Conclusion