scholarly journals 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 ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 626
Author(s):  
John J. Weiland ◽  
Roshan Sharma Poudel ◽  
Alyssa Flobinus ◽  
David E. Cook ◽  
Gary A. Secor ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Mosaic Virus ◽  
Consensus Sequence ◽  
Control Sample ◽  
Yellow Vein ◽  
Tobacco Necrosis Virus ◽  
Cdna Clones ◽  
Polymyxa Betae ◽  
Soilborne Disease ◽  
Satellite Viruses

“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.

scholarly journals Interactions Between Beet necrotic yellow vein virus and Beet soilborne mosaic virus in Sugar Beet

Plant Disease ◽  
2003 ◽  
Vol 87 (10) ◽  
pp. 1170-1175 ◽  
Author(s):  
G. C. Wisler ◽  
R. T. Lewellen ◽  
J. L. Sears ◽  
J. W. Wasson ◽  
H.-Y. Liu ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Mosaic Virus ◽  
Seedling Emergence ◽  
Yellow Vein ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mixed Infections ◽  
Polymyxa Betae ◽  
Susceptible Cultivar ◽  
Fresh Weight ◽  
Virus Content

Soils naturally infested with cultures of aviruliferous Polymyxa betae and viruliferous P. betae carrying two sugar beet benyviruses, Beet necrotic yellow vein virus (BNYVV) and Beet soilborne mosaic virus (BSBMV), alone and in combination, were compared with noninfested soil for their effects on seedling emergence, plant fresh weight, and virus content as measured by enzyme-linked immunosorbent assay (ELISA). Studies examined sugar beet with and without resistance to the disease rhizomania, caused by BNYVV. The Rz gene, conferring resistance to BNYVV, did not confer resistance to BSBMV. BSBMV ELISA values were significantly higher in single infections than in mixed infections with BNYVV, in both the rhizomania-resistant and -susceptible cultivars. In contrast, ELISA values of BNYVV were high (8 to 14 times the healthy mean) in single and mixed infections in the rhizomania-susceptible cultivar, but were low (approximately three times the healthy mean) in the rhizomania-resistant cultivar. Results indicate BNYVV may suppress BSBMV in mixed infections, even in rhizomania-resistant cultivars in which ELISA values for BNYVV are extremely low. Soils infested with P. betae, and with one or both viruses, showed significantly reduced fresh weight of seedlings, and aviruliferous P. betae significantly decreased sugar beet growth in assays.

scholarly journals Spatial Association and Distribution of Beet necrotic yellow vein virus and Beet soilborne mosaic virus in Sugar Beet Fields

Plant Disease ◽  
2003 ◽  
Vol 87 (6) ◽  
pp. 707-711 ◽  
Author(s):  
F. Workneh ◽  
E. Villanueva ◽  
K. Steddom ◽  
C. M. Rush
Keyword(s):  
Sugar Beet ◽  
North Dakota ◽  
Mosaic Virus ◽  
Spatial Patterns ◽  
Spatial Dependence ◽  
Spatial Association ◽  
The United States ◽  
Soil Samples ◽  
Yellow Vein ◽  
Polymyxa Betae

Beet necrotic yellow vein virus (BNYVV) causes rhizomania of sugar beet (Beta vulgaris), which is characterized by stunting, leaf necrosis, constriction of the taproot, and extensive lateral- and feeder-root proliferation. Beet soilborne mosaic virus (BSBMV) causes similar but typically less severe symptoms than those of BNYVV. Both viruses are widely distributed in sugar beet-growing regions of the United States. Both viruses are vectored by the soilborne plasmodiophorid Polymyxa betae Keskin and are very similar in morphology and biology, sharing many characteristics in common. In 1999, soil samples were collected from sugar beet fields in Colorado, Minnesota, North Dakota, and Texas to determine the spatial association and covariation of the viruses in sugar beet fields. In 2000, additional samples were collected from fields in Minnesota and North Dakota. Over the 2-year period, soil samples were collected from 11 fields in various quadrat sizes. The viruses were assayed by growing sugar beet (cv. Beta 1395) in the soil samples and their incidence was determined using the double-antibody sandwich enzyme-linked immunosorbent assay. Both viruses were detected in samples from all fields but were in greater frequencies singly than in association. Association of the two viruses (where both viruses were detected in the same sample or bait plant) varied among fields, ranging from 1 to 42%. Geostatistical analysis revealed that both viruses, in large part, exhibited similar spatial patterns. In all but two fields, there was no spatial dependence among the sampling locations at sampled grid sizes. Their semivariances were constant at all separation distances in all directions indicating random spatial patterns. Overall, the spatial pattern of BNYVV appeared to be a little more structured than that of BSBMV. Even though both viruses are transmitted by the same vector and also exhibited similar distribution patterns, the incidence of one virus may not be estimated from that of the other due to lack of strong association and spatial dependence. However, similarity in spatial patterns of the two suggests that a similar sampling method can be employed for both viruses.

scholarly journals First Report of Rhizomania Disease of Sugar Beet Caused by Beet necrotic yellow vein virus in the Great Lakes Production Region

Plant Disease ◽  
2003 ◽  
Vol 87 (2) ◽  
pp. 201-201 ◽  
Author(s):  
William M. Wintermantel ◽  
Teresa Crook ◽  
Ralph Fogg
Keyword(s):  
Sugar Beet ◽  
Great Lakes ◽  
Beta Vulgaris ◽  
Yellow Vein ◽  
Enzyme Linked Immunosorbent Assay ◽  
Great Lakes Region ◽  
Polymyxa Betae ◽  
Mechanical Inoculation ◽  
Production Region ◽  
Das Elisa

Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV) and vectored by the soilborne fungus Polymyxa betae Keskin, is one of the most economically damaging diseases affecting sugar beet (Beta vulgaris L.). The virus likely originated in Europe and was first identified in California in 1983 (1). It has since spread among American sugar beet production regions in spite of vigorous sanitation efforts, quarantine, and disease monitoring (3). In the fall of 2002, mature sugar beet plants exhibiting typical rhizomania root symptoms, including proliferation of hairy roots, vascular discoloration, and some root constriction (2) were found in several fields scattered throughout central and eastern Michigan. Symptomatic beets were from numerous cultivars, all susceptible to rhizomania. Two to five sugar beet root samples were collected from each field and sent to the USDA-ARS in Salinas, CA for analysis. Hairy root tissue from symptomatic plants was used for mechanical inoculation of indicator plants. Mechanical inoculation produced necrotic lesions on Chenopodium quinoa and systemic infection of Beta vulgaris ssp. macrocarpa, both typical of BNYVV and identical to control inoculations with BNYVV. Symptomatic sugar beet roots were washed and tested using double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) for the presence of BNYVV using standard procedures and antiserum specific for BNYVV (3). Sugar beet roots were tested individually, and samples were considered positive when absorbance values were at least three times those of greenhouse-grown healthy sugar beet controls. Samples were tested from 16 fields, with 10 confirmed positive for BNYVV. Positive samples had mean absorbance values ranging from 0.341 to 1.631 (A405nm) after 30 min. The mean healthy control value was 0.097. Fields were considered positive if one beet tested positive for BNYVV, but in most cases, all beets tested from a field were uniformly positive or uniformly negative. In addition, soil-baiting experiments were conducted on seven of the fields. Sugar beet seedlings were grown in soil mixed with equal parts of sand for 6 weeks and were subsequently tested using DAS-ELISA for BNYVV. Results matched those of the root sampling. Fields testing positive for BNYVV were widely dispersed within a 100 square mile (160 km2) area including portions of Gratiot, Saginaw, Tuscola, and Sanilac counties in the central and eastern portions of the Lower Peninsula of Michigan. The confirmation of rhizomania in sugar beet from the Great Lakes Region marks the last major American sugar beet production region to be diagnosed with rhizomania disease, nearly 20 years after its discovery in California (1). In 2002, there were approximately 185,000 acres (approximately 75,00 ha) of sugar beet grown in the Great Lakes Region, (Michigan, Ohio, and southern Ontario, Canada). The wide geographic distribution of infested fields within the Michigan growing area suggests the entire region should monitor for symptoms, increase rotation to nonhost crops, and consider planting rhizomania resistant sugar beet cultivars to infested fields. References:(1) J. E. Duffus et al. Plant Dis. 68:251, 1984. (2) J. E. Duffus. Rhizomania. Pages 29–30 in: Compendium of Beet Diseases and Insects, E. D. Whitney and J. E. Duffus eds. The American Phytopathological Society, St. Paul, MN, 1986. (3) G. C. Wisler et al. Plant Dis. 83:864, 1999.

scholarly journals Characteristics of Beet Soilborne Mosaic Virus, a Furo-like Virus Infecting Sugar Beet

Plant Disease ◽  
1997 ◽  
Vol 81 (9) ◽  
pp. 1070-1076 ◽  
Author(s):  
G. B. Heidel ◽  
C. M. Rush ◽  
T. L. Kendall ◽  
S. A. Lommel ◽  
R. C. French
Keyword(s):  
Sugar Beet ◽  
Molecular Mass ◽  
Host Range ◽  
Mosaic Virus ◽  
Gel Electrophoresis ◽  
Polymyxa Betae ◽  
Northern Blots ◽  
Variable Size ◽  
Western Blots ◽  
Rigid Rod

Beet soilborne mosaic virus (BSBMV) is a rigid rod-shaped virus transmitted by Polymyxa betae. Particles were 19 nm wide and ranged from 50 to over 400 nm, but no consistent modal lengths could be determined. Nucleic acids extracted from virions were polyadenylated and typically separated into three or four discrete bands of variable size by agarose-formaldehyde gel electrophoresis. RNA 1 and 2, the largest of the RNAs, consistently averaged 6.7 and 4.6 kb, respectively. The sizes and number of smaller RNA species were variable. The molecular mass of the capsid protein of BSBMV was estimated to be 22.5 kDa. In Northern blots, probes specific to the 3′ end of individual beet necrotic yellow vein virus (BNYVV) RNAs 1–4 hybridized strongly with the corresponding BNYVV RNA species and weakly with BSBMV RNAs 1, 2, and 4. Probes specific to the 5′ end of BNYVV RNAs 1–4 hybridized with BNYVV but not with BSBMV. No cross-reaction between BNYVV and BSBMV was detected in Western blots. In greenhouse studies, root weights of BSBMV-infected plants were significantly lower than mock-inoculated controls but greater than root weights from plants infected with BNYVV. Results of serological, hybridization, and virulence experiments indicate that BSBMV is distinct from BNYVV. However, host range, capsid size, and the number, size, and polyadenylation of its RNAs indicate that BSBMV more closely resembles BNYVV than it does other members of the genus Furovirus.

scholarly journals Distribution and Molecular Characterization of Resistance-Breaking Isolates of Beet necrotic yellow vein virus in the United States

Plant Disease ◽  
2007 ◽  
Vol 91 (7) ◽  
pp. 847-851 ◽  
Author(s):  
H.-Y. Liu ◽  
R. T. Lewellen
Keyword(s):  
United States ◽  
Amino Acids ◽  
Sugar Beet ◽  
The United States ◽  
Field Trials ◽  
Yellow Vein ◽  
Polymyxa Betae ◽  
Imperial Valley ◽  
Resistance Breaking ◽  
Soil Surveys

Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania in sugar beet (Beta vulgaris). The virus is transmitted by the plasmodiophorid Polymyxa betae. The disease is controlled primarily by the use of partially resistant cultivars. During 2003 and 2004 in the Imperial Valley of California, partially resistant sugar beet cultivars with Rz1 allele seemed to be compromised. Field trials at Salinas, CA have confirmed that Rz1 has been defeated by resistance-breaking isolates. Distinct BNYVV isolates have been identified from these plants. Rhizomania-infested sugar beet fields throughout the United States were surveyed in 2004–05. Soil surveys indicated that the resistance-breaking isolates not only existed in the Imperial Valley and San Joaquin Valley of California but also in Colorado, Idaho, Minnesota, Nebraska, and Oregon. Of the soil samples tested by baited plant technique, 92.5% produced infection with BNYVV in ‘Beta 6600’ (rz1rz1rz1), 77.5% in ‘Beta 4430R’ (Rz1rz1), 45.0% in ‘Beta G017R’ (Rz2rz2), and 15.0% in ‘KWS Angelina’ (Rz1rz1+Rz2rz2). Analyses of the deduced amino acid sequence of coat protein and P-25 protein of resistance-breaking BNYVV isolates revealed the high percentage of identity with non-resistance-breaking BNYVV isolates (99.9 and >98.0%, respectively). The variable amino acids in P-25 proteins were located at the residues of 67 and 68. In the United States, the two amino acids found in the non-resistance-breaking isolates were conserved (AC). The resistance-breaking isolates were variable including, AF, AL, SY, VC, VL, and AC. The change of these two amino acids cannot be depended upon to differentiate resistance-breaking and non-resistance-breaking isolates of BNYVV.

scholarly journals First Report of Beet necrotic yellow vein virus on Red Table Beet in Brazil

Plant Disease ◽  
2015 ◽  
Vol 99 (3) ◽  
pp. 423-423 ◽  
Author(s):  
J. A. M. Rezende ◽  
V. M. Camelo ◽  
D. Flôres ◽  
A. P. O. A. Mello ◽  
E. W. Kitajima ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sugar Beet ◽  
Hairy Root ◽  
Contaminated Soil ◽  
The United States ◽  
Amino Acid Sequences ◽  
Yellow Vein ◽  
Polymyxa Betae ◽  
Rt Pcr ◽  
First Report

Beet necrotic yellow vein virus (BNYVV) is an economically important pathogen of sugar beet (Beta vulgaris var. saccharifera) in several European, and Asian countries and in the United States (3). The virus is transmitted by the soil-inhabiting plasmodiophorid Polymyxa betae and causes the rhizomania disease of sugar beet. In November 2012, plants of B. vulgaris subsp. vulgaris cv. Boro (red table beet) exhibiting mainly severe characteristic root symptom of rhizomania were found in a commercial field located in the municipality of São José do Rio Pardo, State of São Paulo, Brazil. No characteristic virus-inducing foliar symptom was observed on diseased plants. The incidence of diseased plants was around 70% in the two visited crops. As the hairy root symptom is indicative of infection by BNYVV, the present study aimed to detect and identify this virus associated with the diseased plants. Preliminary leaf dip analysis by transmission electron microscopy revealed the presence of very few benyvirus-like particles. Total RNA was extracted from roots of three symptomatic plants and one asymptomatic plant according to Toth et al. (3). One-step reverse-transcription–polymerase chain reaction (RT-PCR) was performed as described by Morris et al. (2) with primers that amplify part of the coat protein gene at RNA2. The initial assumption that the hairy root symptom was associated with BNYVV infection was confirmed by the amplification of a fragment of ~500 bp from all three symptomatic samples. No amplicon was obtained from the asymptomatic control plant. Amplicons were directly sequenced, and the consensus nucleotide and deduced amino acid sequences showed 100% identity. The nucleotide sequence for one amplicon (Accession No. KM433683) was compared with other sequences deposited in GenBank. The nucleotide (468 nt) and deduced amino acid (156 aa) sequences shared 93 to 100 and 97 to 99% identity, respectively with the corresponding nucleotide and amino acid sequences for other isolates of type A of BNYVV. The virus was transmitted to three of 10 red table beet plants inoculated with contaminated soil, and infection was confirmed by nested RT-PCR, as described by Morris et al. (1), and nucleotide sequencing. This is the first report on the occurrence of BNYVV in Brazil, which certainly will affect the yield of red table beet in the producing region. Therefore, mapping of the occurrence of BNYVV in red table beet-producing areas in Brazil for containment of the spread of the virus is urgent. In the meantime, precautions should be taken to control the movement of contaminated soil and beet roots, carrots, or any vegetable grown on infested land that might introduce the virus to still virus-free regions. References: (1) J. Morris et al. J. Virol. Methods 95:163, 2001. (2) D. D. Sutic et al. Handbook of Plant Virus Diseases. CRC Press, Boca Raton, Florida, 1999. (3) I. K. Toth et al. Methods for the Detection and Quantification of Erwinia carotovora subsp. atroseptica (Pectobacterium carotovorum subsb. atrosepticum) on Potatoes: A Laboratory Manual. Scottish Crop Research Institute, Dundee, Scotland, 2002.

scholarly journals Biological properties of Beet soil-borne mosaic virus and Beet necrotic yellow vein virus cDNA clones produced by isothermal in vitro recombination: Insights for reassortant appearance

Virology ◽  
2018 ◽  
Vol 518 ◽  
pp. 25-33 ◽  
Author(s):  
Marlene Laufer ◽  
Hamza Mohammad ◽  
Edgar Maiss ◽  
Katja Richert-Pöggeler ◽  
Mattia Dall'Ara ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Biological Properties ◽  
Yellow Vein ◽  
Cdna Clones ◽  
In Vitro Recombination ◽  
Virus Cdna

scholarly journals Multiplex Reverse Transcription-PCR for Simultaneous Detection of Beet Necrotic Yellow Vein Virus, Beet Soilborne Virus, and Beet Virus Q and Their Vector Polymyxa betae KESKIN on Sugar Beet

2003 ◽  
Vol 69 (4) ◽  
pp. 2356-2360 ◽  
Author(s):  
Alexandre Meunier ◽  
Jean-François Schmit ◽  
Arnaud Stas ◽  
Nazli Kutluk ◽  
Claude Bragard
Keyword(s):  
Sugar Beet ◽  
Reverse Transcription ◽  
Detection Threshold ◽  
Simultaneous Detection ◽  
Yellow Vein ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymyxa Betae ◽  
Reverse Transcription Pcr ◽  
Soilborne Viruses ◽  
Beet Virus Q

ABSTRACT Three soilborne viruses transmitted by Polymyxa betae KESKIN in sugar beet have been described: Beet necrotic yellow vein virus (BNYVV), the agent of rhizomania, Beet soilborne virus (BSBV), and Beet virus Q (BVQ). A multiplex reverse transcription-PCR technique was developed to simultaneously detect BNYVV, BSBV, and BVQ, together with their vector, P. betae. The detection threshold of the test was up to 128 times greater than that of an enzyme-linked immunosorbent assay. Systematic association of BNYVV with one or two different pomoviruses was observed. BVQ was detected in samples from Belgium, Bulgaria, France, Germany, Hungary, Italy, Sweden, and The Netherlands but not in samples from Turkey.

scholarly journals A single U/C nucleotide substitution changing alanine to valine in the beet necrotic yellow vein virus P25 protein promotes increased virus accumulation in roots of mechanically inoculated, partially resistant sugar beet seedlings

2009 ◽  
Vol 90 (3) ◽  
pp. 759-763 ◽  
Author(s):  
R. Koenig ◽  
S. Loss ◽  
J. Specht ◽  
M. Varrelmann ◽  
P. Lüddecke ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Nucleotide Substitution ◽  
Starting Material ◽  
Biologically Active ◽  
Yellow Vein ◽  
Local Lesion ◽  
Cdna Clones ◽  
Coding Sequences ◽  
Virus Accumulation ◽  
Sequence Variations

Beet necrotic yellow vein virus (BNYVV) A type isolates E12 and S8, originating from areas where resistance-breaking had or had not been observed, respectively, served as starting material for studying the influence of sequence variations in BNYVV RNA 3 on virus accumulation in partially resistant sugar beet varieties. Sub-isolates containing only RNAs 1 and 2 were obtained by serial local lesion passages; biologically active cDNA clones were prepared for RNAs 3 which differed in their coding sequences for P25 aa 67, 68 and 129. Sugar beet seedlings were mechanically inoculated with RNA 1+2/RNA 3 pseudorecombinants. The origin of RNAs 1+2 had little influence on virus accumulation in rootlets. E12 RNA 3 coding for V67C68Y129 P25, however, enabled a much higher virus accumulation than S8 RNA 3 coding for A67H68H129 P25. Mutants revealed that this was due only to the V67 ‘G U U’ codon as opposed to the A67 ‘G C U’ codon.

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