Genetic diversity and population structure of beet necrotic yellow vein virus in China

Zhuo, Na; Jiang, Ning; Zhang, Chao; Zhang, Zongying; Zhang, Guozhen; Han, Chenggui; Wang, Ying

doi:10.1016/j.virusres.2015.05.009

Cited by 12 publications

(18 citation statements)

References 40 publications

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“…Several prior investigations utilized sequences of RNAs 3 and 4 for the purposes of categorizing the genetic diversity of BNYVV and ascertaining the origins of the US isolates based on these sequences. We here confirm the grouping proposed by Chiba et al [ 25 ], Schirmer et al [ 34 ], and Zhuo et al [ 35 ], in which US isolates of BNYVV nationwide appear to group with those of the A-types from Italy ( Figure 2 ; Table 2 ). Although the basis for this apparent relatedness is unknown, it is possible that the virus made its way into US sugar beet production fields through international transit of infested plant material or soil.…”

Section: Discussionsupporting

confidence: 92%

“…The most common tetrad amino acids (AAs) observed in the samples of the present study included VCHG, ACHG, VLHG, and TLHG, the first three of which have a prior association with the breaking of Rz1-gene-based resistance in sugar beet [ 5 , 14 , 17 ]. All sequences were used to confirm the placement of the BNYVV-US within phylogenetic groupings ( Figure 2 ) previously reported by Chiba et al [ 25 ], Schirmer et al [ 34 ], and Zhuo et al [ 35 ]. Through the ranking of similarity with previous sequences already used in phylogenetic group formation ( Table 2 ; Figure 2 ), the lineage of the US isolates obtained based on sequence analysis was in broad agreement with the results of these prior analyses, indicating that these viruses are of the A-type designation.…”

Section: Resultsmentioning

confidence: 88%

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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

Weiland

Poudel

Flobinus

et al. 2020

Viruses

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“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.

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Section: Discussionsupporting

confidence: 92%

Section: Resultsmentioning

confidence: 88%

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

Weiland

Poudel

Flobinus

et al. 2020

Viruses

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“…RNA5‐containing BNYVV has been prevalent for a long time in Japan and China (Chiba et al ., 2011; Zhuo et al ., 2015; Tamada et al ., 2016), and recently has been found to have spread widely from an originally limited area in Europe (Galein et al ., 2018) and also the Middle East (Yilmaz et al ., 2016). RNA5 is known to be associated with symptom severity of the virus (Tamada et al ., 1996; Heijbroek et al ., 1999), but little is known about its function.…”

Section: Discussionmentioning

confidence: 99%

“…Six other strains (belonging to the A‐II or A‐I types), that is, Japan D, Japan O, France P (= P type), China B, China H, and China X, originally isolated from Japan, France, and China, were found in limited areas with a few exceptions. Most isolates of these six strains contain RNA5 (Koenig and Lennefors, 2000; Chiba et al ., 2011; Zhuo et al ., 2015; Tamada et al ., 2016). Recently, RNA5‐containing BNYVV, which was phylogenetically closer to the Japanese isolates than the P‐type isolates, was reported to be prevalent in Turkey (Yilmaz et al ., 2016, 2018).…”

Section: Introductionmentioning

confidence: 99%

Pathogenetic roles of beet necrotic yellow vein virus RNA5 in the exacerbation of symptoms and yield reduction, development of scab‐like symptoms, and Rz1‐resistance breaking in sugar beet

Tamada

Uchino

Kusume³

et al. 2020

Plant Pathology

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Beet necrotic yellow vein virus (BNYVV) generally has a four-segmented positivesense RNA genome (RNAs 1-4), but some European and most Asian strains have an additional segment, RNA5. This study examined the effect of RNA5 and RNA3 on different sugar beet cultivars using a Polymyxa-mediated inoculation system under field and laboratory conditions. In field tests, the degree of sugar yield served as an index for assessing the virulence of BNYVV strains. Japanese A-II type isolates without RNA5 caused mostly 15%-90% sugar yield reductions, depending on the susceptibility of sugar beet cultivars, whereas the isolates with RNA5 induced more than 90% yield losses in the seven susceptible cultivars, but small yield losses in one Rz1-resistant and Rizor cultivars. However, a laboratory-produced isolate containing RNA5 but lacking RNA3 caused higher yield losses in Rizor than in susceptible plants, and induced scab-like symptoms on the root surface of both susceptible and resistant plants. In laboratory tests, A-II type isolates without RNA5 had low viral RNA accumulation levels in roots of Rizor and Rz1-resistant plants at early stages of infection, but in the presence of RNA5, viral RNA3 accumulation levels increased remarkably. This increased RNA3 accumulation was not observed in roots of the WB42 accession with the Rz2 gene. In contrast, the presence of RNA3 did not affect RNA5 accumulation levels. Collectively, this study demonstrated that RNA5 is involved in the development of scab-like symptoms and the enhancement of RNA3 accumulation, and suggests these characteristics of RNA5 are associated with Rz1-resistance breaking.

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“…BNYVV type P was first found in a restricted area in France, UK, Germany and Kazakhstan, while type J is present in Asia and Japan and was identified once in Germany (Koenig et al, 2008). Phylogenetic studies of BNYVV isolates from different geographic areas in China (Zhuo et al, 2015) demonstrated gene flow between distant populations indicating that BNYVV populations are not geographically differentiated. A recent study from Turkey (Y € uksel € Ozmen et al, 2020) revealed the emergence of novel variants from genetic reassortment of genome components RNA-2 and RNA-3 derived from the European A type and an RNA-5 related to the East Asian type J.…”

Section: Intraspecific Diversitymentioning

confidence: 99%

Pest categorisation of beet necrotic yellow vein virus

Dehnen‐Schmutz¹,

Serio²,

Gonthier³

et al. 2020

EFS2

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Following a request from the EU Commission, the Panel on Plant Health performed a categorisation of beet necrotic yellow vein virus ( BNYVV ), the causal agent of the sugar beet rhizomania disease. The virus is currently listed in Annex III as a protected zone ( PZ ) quarantine pest of the Commission Implementing Regulation ( EU ) 2019/2072. The identity of the BNYVV is well established. BNYVV is a soil‐borne virus transmitted by the obligate root plasmodiophorid endoparasite Polymyxa betae . BNYVV is widely distributed in the EU , but is not reported in the following EU PZ s: Ireland, France (Brittany), Portugal (Azores), Finland and Northern Ireland. The virus may enter, become established and spread in the PZ s via P. betae resting spores with soil and growing media as such or attached to machinery and with roots and tubercles of species other than B. vulgaris and with plants for planting. Introduction of BNYVV would have a negative impact on sugar beet and other beet crops in PZ s, because of yield and sugar content reduction. Phytosanitary measures are available to reduce the likelihood of entry and spread in the PZ s. Once the virus and its plasmodiophorid vector have entered a PZ , their eradication would be difficult due to the persistence of viruliferous resting spores in the soil. The main knowledge gaps or uncertainties identified concerning the presence of BNYVV in the PZ s and the incidence and distribution of BNYVV in Switzerland, a country to which a range of specific requirements do not apply. BNYVV meets all the criteria that are within the remit of EFSA to qualify as a potential protected zone union quarantine pest. Plants for planting are not considered as a main means of spread, and therefore BNYVV does not satisfy all the criteria evaluated by EFSA to qualify as potential Union regulated non‐quarantine pest.

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Genetic diversity and population structure of beet necrotic yellow vein virus in China

Cited by 12 publications

References 40 publications

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

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

Pathogenetic roles of beet necrotic yellow vein virus RNA5 in the exacerbation of symptoms and yield reduction, development of scab‐like symptoms, and Rz1‐resistance breaking in sugar beet

Pest categorisation of beet necrotic yellow vein virus

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