Analysis of the complete genome of a virus associated with twisted leaf disease of cherry reveals evidence of a close relationship to unassigned viruses in the family Betaflexiviridae

James, D.; Varga, Á.; Lye, David C.

doi:10.1007/s00705-014-2075-6

Cited by 9 publications

(4 citation statements)

References 23 publications

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“…The situation of APV1 and APV3 is more complex, since sequence comparisons using the polymerase and coat protein genes or their deduced amino acid sequences provide a conflicting picture, with divergence levels suggesting the existence of a single or of two species, respectively. Although molecular criteria based on identity level in the polymerase and in the coat protein genes are usually convergent [ 21 ], such a situation of conflict between polymerase and coat protein criteria has been observed previously for a few Foveaviruses [ 18 , 22 , 23 ] or for unassigned members in the family Betaflexiviridae [ 24 ]. In such cases, the use of additional biological information such as serology, host range, associated symptoms, or vector transmission has been used to reach a decision on the species status.…”

Section: Discussionmentioning

confidence: 99%

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

2016

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Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.

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Section: Discussionmentioning

confidence: 99%

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

2016

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“…During the last five years, a number of viral species belonging to the family Betaflexiviridae have been characterized by either classical approaches (e.g. [1–9]) or using high-throughput next generation sequencing (NGS) technologies [10–12]. In the later case, different strategies have been used, targeting different nucleic acid templates (single-stranded or double-stranded RNAs, small interfering RNAs, messenger RNAs, partially or completely purified viral particles) or the sequencing technology (Illumina or 454 pyrosequencing [13–17]).…”

Section: Introductionmentioning

confidence: 99%

Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution

et al. 2015

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Double stranded RNAs from Prunus samples gathered from various surveys were analyzed by a deep-sequencing approach. Contig annotations revealed the presence of a potential new viral species in an Azerbaijani almond tree (Prunus amygdalus) and its genome sequence was completed. Its genomic organization is similar to that of the recently described Apricot vein clearing associated virus (AVCaV) for which two new isolates were also characterized, in a similar fashion, from two Japanese plums (Prunus salicina) from a French germplasm collection. The amino acid identity values between the four proteins encoded by the genome of the new virus have identity levels with those of AVCaV which fall clearly outside the species demarcation criteria. The new virus should therefore be considered as a new species for which the name of Caucasus prunus virus (CPrV) has been proposed. Phylogenetic relationships and nucleotide comparisons suggested that together with AVCaV, CPrV could define a new genus (proposed name: Prunevirus) in the family Betaflexiviridae. A molecular test targeting both members of the new genus was developed, allowing the detection of additional AVCaV isolates, and therefore extending the known geographical distribution and the host range of AVCaV. Moreover, the phylogenetic trees reconstructed with the amino acid sequences of replicase, movement and coat proteins of representative Betaflexiviridae members suggest that Citrus leaf blotch virus (CLBV, type member of the genus Citrivirus) may have evolved from a recombination event involving a Prunevirus, further highlighting the importance of recombination as a driving force in Betaflexiviridae evolution. The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers KM507061-KM504070.

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“…In studies aiming to elucidate the aetiology of the rusty mottle and twisted leaf diseases of cherry, two new viruses have been characterised (named Cherry rusty mottle associated virus , CRMaV, and Cherry twisted leaf associated virus , CTLaV, respectively) and proposed to define a new genus Robigovirus in the Betaflexiviridae family. This genus, recently accepted by the ICTV, includes other two very well‐known Prunus viruses ( Cherry necrotic rusty mottle virus , CNRMV, and Cherry green ring mottle virus , CGRMV) (Villamor & Eastwell, ; James et al ., ; Villamor et al ., ). The two species CNRMV and CGRMV are already accepted as species of genus Robigovirus by the ICTV since 2016.…”

Section: Identification Incidence and Genetic Variability Of New Isomentioning

confidence: 98%

Recent advances and prospects in Prunus virology

Rubio

Martínez‐Gómez

Marais

et al. 2017

Annals of Applied Biology

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The stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high-throughput sequencing data generated for plant genomics-oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus-host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change. © 2017 Association of Applied Biologists Prunus virology M. Rubio et al.

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Analysis of the complete genome of a virus associated with twisted leaf disease of cherry reveals evidence of a close relationship to unassigned viruses in the family Betaflexiviridae

Cited by 9 publications

References 23 publications

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution

Recent advances and prospects in Prunus virology

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