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Špak J, Koloniuk I, Tzanetakis IE. Graft-Transmissible Diseases of Ribes - Pathogens, Impact, and Control. PLANT DISEASE 2021; 105:242-250. [PMID: 32870112 DOI: 10.1094/pdis-04-20-0759-fe] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This article provides an up-to-date review of disease-causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact, and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia, and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Candidatus Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.
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Affiliation(s)
- Josef Špak
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Igor Koloniuk
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
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Complete genome sequence of a novel capillovirus infecting Hevea brasiliensis in China. Arch Virol 2019; 165:249-252. [PMID: 31748875 DOI: 10.1007/s00705-019-04459-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
Tapping panel dryness (TPD) is a complex disorder that causes partial or complete cessation of latex drainage upon tapping of rubber trees (Hevea brasiliensis). In this work, we determined the complete genome sequences of a novel virus identified in a rubber tree with TPD syndrome in China. The genome of the virus consists of 6811 nt and possesses two overlapping open reading frames (ORF1 and ORF2), encoding a polyprotein and a movement protein, respectively. The polyprotein shares 37% amino acid sequence identity with cherry virus A (CVA, ARQ83874.1) over 99% coverage. The genome architecture is similar to that of members of the genus Capillovirus (family Betaflexiviridae). Phylogenetic analysis of the replicase proteins showed that the virus clustered together with members of the genus Capillovirus. The new virus is tentatively called "rubber tree virus 1" (RTV1). RTV1 is the first virus reported to infect rubber trees. This work lays a foundation for research into finding the potential causal agent of TPD in Hevea brasiliensis.
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Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization. Arch Virol 2019; 165:223-226. [PMID: 31655850 DOI: 10.1007/s00705-019-04444-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
Analysis of a loquat tree with leaf curl symptoms by deep sequencing revealed a novel virus with a single-stranded RNA genome, for which the name "loquat virus A" (LoVA) was proposed. The complete genome sequence comprised 7553 nucleotides (nt) and an additional poly(A) tail at the 3' terminus. Sequence comparisons of LoVA showed moderate similarity to cherry virus A (CVA), currant virus A (CuVA), and mume virus A (MuVA), which are members of the genus Capillovirus in the family Betaflexiviridae. Phylogenetic analysis of the full-genome nt sequence and replicase-like protein supported the placement of LoVA within the genus Capillovirus. However, it has a distinct genome organization, differing from recognized capilloviruses, as it contains three open reading frames (ORFs), with the coat protein (CP) expressed separately from the replication-associated protein (RP) rather than being encoded in the same ORF. This indicates that LoVA is a novel member of the genus Capillovirus in the family Betaflexiviridae with a distinct genomic organization.
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Liu H, Wu L, Zheng L, Cao M, Li R. Characterization of three new viruses of the family Betaflexiviridae associated with camellia ringspot disease. Virus Res 2019; 272:197668. [DOI: 10.1016/j.virusres.2019.197668] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 10/26/2022]
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, der Werf WV, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Winter S, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. 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. EFSA J 2019; 17:e05501. [PMID: 32626418 PMCID: PMC7009187 DOI: 10.2903/j.efsa.2019.5501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
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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Koloniuk I, Thekke-Veetil T, Reynard JS, Mavrič Pleško I, Přibylová J, Brodard J, Kellenberger I, Sarkisova T, Špak J, Lamovšek J, Massart S, Ho T, Postman JD, Tzanetakis IE. Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species. Viruses 2018; 10:E369. [PMID: 30002359 PMCID: PMC6071065 DOI: 10.3390/v10070369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
Abstract
Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.
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Affiliation(s)
- Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | | | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Jaroslava Přibylová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Justine Brodard
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland.
| | | | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Josef Špak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Janja Lamovšek
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium.
| | - Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Joseph D Postman
- National Clonal Germplasm Repository, United States Department of Agriculture, Corvallis, OR 97333, USA.
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume). Viruses 2018; 10:v10040144. [PMID: 29570605 PMCID: PMC5923438 DOI: 10.3390/v10040144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunusmume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed.
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