Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease

He, Yan; Yang, Zuokun; Hóng, Ní; Wang, Guoping; Ning, Guogui; Xú, Wénxìng

doi:10.1111/mpp.12202

Cited by 35 publications

(14 citation statements)

References 51 publications

(66 reference statements)

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“…HTS does not require any previous knowledge of viral sequences and can sequence millions or billions of DNA molecules in parallel, enabling the detection of all viruses present in a plant (virome), including those still unknown ( Roossinck, 2015 ). HTS allowed elucidating the elusive etiology of some diseases ( Vives et al., 2013 ; He et al., 2015 ), but often it is not possible to find a direct association between the disease and a particular virus ( Tomašechová et al., 2020 ) among those detected in the infected plant. In this case, the diagnostic must be established by fulfilling Koch’s postulates, or at least by finding a tight association between the disease and the presence of a certain virus in field surveys ( Mumo et al., 2020 ).…”

Section: Detection Of Plant Virusesmentioning

confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

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Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.

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Section: Detection Of Plant Virusesmentioning

confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

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“…The RdRp is produced as a fusion ORF1ab by the +1 ribosomal frameshift at the end of ORF1. In addition, unique ORFs that are shared by some members are also observed (Karasev et al, 1995;Tzanetakis et al, 2007;He et al, 2015;Agranovsky, 2016;Zheng et al, 2018).…”

Section: Introductionmentioning

confidence: 96%

Two novel closteroviruses, fig virus A and fig virus B, identified by the analysis of the high-throughput RNA-sequencing data of fig (Ficus carica) latex

Park¹,

Goh²,

Hahn³

2021

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Closteroviruses (genus Closterovirus, family Closteroviridae) are RNA viruses that infect and cause viral diseases in many economically important plants. Genome sequences of two novel closteroviruses named fig virus A (FiVA) and fig virus B (FiVB) were identified in high-throughput sequencing data obtained from a fig latex sample. FiVA and FiVB genomes, whose lengths are 19,333 bp and 18,741 bp, respectively, were predicted to have 14 shared open reading frames, nine of which had homologs in other closteroviruses. Phylogenetic analysis confirmed that FiVA and FiVB are novel closteroviruses forming a strong subclade with fig mild mottle-associated virus within the genus Closterovirus. FiVA and FiVB genome sequences identified in this study are useful resources for investigating the evolution of closterovirus genome organization.

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“…Antiviral defense in plants involves the degradation of viral RNA by DICER to 21–24 nt-long RNA populations. Sequencing of these smRNAs would allow the assembly of entire viral genome(s); although, in reality, because of the nonrandom distribution of these smRNAs over the genome, contigs often cover a portion of the viral genome at best, and the sequence reconstruction of complete genomes is rarely accomplished [6, 3, 7, 8]. Furthermore, repetitive sequences or sequence variations make it difficult to assemble complete genomes with a high level of confidence.…”

Section: Introductionmentioning

confidence: 99%

Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences

2019

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Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus .

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Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease

Cited by 35 publications

References 51 publications

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

Two novel closteroviruses, fig virus A and fig virus B, identified by the analysis of the high-throughput RNA-sequencing data of fig (Ficus carica) latex

Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences

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