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

Authors: Weiland, John; SHARMA POUDEL, ROSHAN - North Dakota State University; FLOBINUS, ALYSSA - North Dakota State University; COOK, DAVID - North Dakota State University; SECOR, GARY - North Dakota State University; Bolton, Melvin

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/9/2020
Publication Date: 6/10/2020
Citation: Weiland, J.J., Sharma Poudel, R., Flobinus, A., Cook, D., Secor, G., Bolton, M.D. 2020. 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. Viruses. 12(6):626. https://doi.org/10.3390/v12060626.
DOI: https://doi.org/10.3390/v12060626

Interpretive Summary: ‘Rhizomania’ is one of the most important diseases facing the sugar beet industry. The disease is caused by a virus named beet necrotic yellow vein virus (BNYVV), which is transmitted to plants by an organism called Polymyxa betae. Rhizomania is managed worldwide by a handful of resistance genes that have been incorporated by plant breeders to make plants resistant to the virus. While these resistance genes have been very helpful for many years, they are starting to break down resulting in disease development. Analysis of so-called 'resistance-breaking' strains of BNYVV have identified certain regions in the BNYVV genome that appear to be related to the ability to overcome resistance genes. Nevertheless, many questions remain regarding the full nature of resistance-breaking by BNYVV in sugar beet, the extent to which the P. betae vector plays a role in disease aggressiveness, and the degree to which other known, and possibly unknown, viruses in the sugar beet root infection court could positively or negatively impact disease. In the present study, samples from diseased sugar beet seedlings and adult plants were subjected to a technology called RNA sequencing (RNAseq) that enabled the identification of any and all RNA viruses in the sugar beet root. As expected, analysis of the sequencing data from this exercise identified BNYVV. Additionally, we identified other sugarbeet viruses as well as novel putative viruses. Based on the derived BNYVV sequence and that of a novel Necrovirus, we developed cDNA clones that were infectious to test plants, validating the integrity of the RNASeq approach used in this study. With the additional discovery of potentially novel satellite viruses, the results confirm the usefulness of the method in assessing the spectrum of viruses present in sugar beet plants exhibiting rhizomania disease.

Technical Abstract: ‘Rhizomania’ of sugar beet is a soil-borne disease complex comprised of beet necrotic yellow vein virus (BNYVV) and its plasmodiophorid vector Polymyxa betae. Although BNYVV is consider 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 3,682 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.