Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine

Jo, Yeonhwa; Song, Myung-Kyu; Choi, Hoseong; Park, Jae-Seong; Lee, Jae-Wung; Lian, Sen; Lee, Bong Choon; Cho, Won Kyong

doi:10.1128/genomea.00994-17

Cited by 27 publications

(11 citation statements)

References 9 publications

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“…In all grapevine accessions, contigs of 7031 to 7552 nt in length and coverage between 4.1× to 7136× (MF781081, MF993573, MF993574, and MF993575) were variants of grapevine virus G (GVG) [13]. One contig from vine VLJ-178 (MF993576) of 7,428 nt and 280× coverage had 90% query coverage and 76% nt sequence identity to a sequence of grapevine virus K (GVK) [14] and 9% query coverage with 87% nt sequence identity with grapevine virus D (GVD) ORF1 and ORF2 (Y07764). Two other contigs from vine VLJ-178 (MG001925) and three from vine VB-108 (MG001926) showed the highest nucleotide sequence similarity to grapevine virus T (GVT) [15].…”

Section: Resultsmentioning

confidence: 99%

Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones

Vončina

Almeida

2018

Arch Virol

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Next-generation sequencing of total RNA samples from four Croatian autochthonous grapevine varieties revealed the presence of a novel virus in two grapevine accessions. The complete genome sequence of a novel virus, tentatively named "grapevine badnavirus 1" (GBV-1), was reconstructed from a de novo-assembled contig. GBV-1 has a genome of 7,145 nucleotides containing three ORFs with sequence similarity to other badnaviruses. In addition, several other viruses and viroids, including grapevine virus G, grapevine virus K/D, grapevine virus T, grapevine Roditis leaf discoloration-associated virus, grapevine yellow speckle viroids 1 and 2, and hop stunt viroid were detected and identified for the first time in Croatian grapevines in the course of this study.

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Section: Resultsmentioning

confidence: 99%

Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones

Vončina

Almeida

2018

Arch Virol

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“…Leafroll-associated viruses are often detected along with the presence of other betaflexivirids such as vitiviruses [Grapevine virus A (GVA) [44], Grapevine virus B (GVB) [20], Grapevine virus D (GVD1) [1], Grapevine virus E (GVE) [47], Grapevine virus F (GVF) [4] and newly describribed vitiviruses tentatively named Grapevine virus G (GVG) [8], Grapevine virus H (GVH) [12], Grapevine virus I (GVI) [7], Grapevine virus K (GVK) [30] and Grapevine virus T (GVT) [31]. The foveavirus grapevine rupestris stem pitting-associated virus (GRSPaV) [42], also belonging to the Betaflexiviridae family is the most prevalent ssRNA grapevine virus worldwide.…”

Section: Introductionmentioning

confidence: 99%

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

et al. 2018

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We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.

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“…() Grapevine virus K * GVKXNot a valid species it is being synonymised with GVDSee GVDJo et al. () Grapevine virus T * GVTXVirus reported from HTS data in Korea on a grapevine of Italian origin. Virus also reported in Germany and known by expert knowledge to be present in FranceLimited uncertainty.…”

Section: Appendix B – Viruses and Viroids Of Cydonia Mill Fragaria mentioning

confidence: 99%

List of non‐EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L.

Bragard¹,

Dehnen‐Schmutz²,

Gonthier³

et al. 2019

EFS2

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The Panel on Plant Health performed a listing of non-EU viruses and viroids (reported hereinafter as viruses) of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review identified 197 viruses infecting one or more of the host genera under consideration. Viruses were allocated into three categories (i) 86 non-EU viruses, known to occur only outside the EU or having only limited presence in the EU (i.e. reported in only one or few Member States (MSs), known to have restricted distribution, outbreaks), (ii) 97 viruses excluded at this stage from further categorisation efforts because they have significant presence in the EU (i.e. only reported so far from the EU or known to occur or be widespread in some MSs or frequently reported in the EU), (iii) 14 viruses with undetermined standing for which available information did not readily allow to allocate to one or the other of the two above groups. Comments provided by MSs during consultation phases were integrated in the opinion. The main knowledge gaps and uncertainties of this listing concern (i) the geographic distribution and prevalence of the viruses analysed, in particular when they were recently described; (ii) the taxonomy and biological status of a number of poorly characterised viruses; (iii) the host status of particular plant genera in relation to some viruses. The viruses considered as non-EU and those with undetermined standing will be categorised in the next steps to answer a specific mandate from the Commission to develop pest categorisations for non-EU viruses. This list does not imply a prejudice on future needs for a pest categorisation for other viruses which are excluded from the current categorisation efforts.

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Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine

Cited by 27 publications

References 9 publications

Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones

Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

List of non‐EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L.

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