ArticlePloS one2014
De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
42 citing papers in PubMed, 104 citations in OpenAlex.
- Deep Sequencing Analysis of Virome Components, Viral Gene Expression and Antiviral RNAi Responses inInternational journal of molecular sciences · 2024Article
- Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding.Viruses · 2024Article
- Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran.Viruses · 2024Article
- Cannabis Virome Reconstruction and Antiviral RNAi Characterization through Small RNA Sequencing.Plants (Basel, Switzerland) · 2023Article
- Molecular Characterization of Three Apple Geminivirus Isolates in Crabapples Detected in Inner Mongolia, China.Plants (Basel, Switzerland) · 2023Article
- Virus Elimination from Naturally Infected Field Cultivars of Potato (International journal of molecular sciences · 2022Article
- A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses.Microorganisms · 2021Review
- Endogenous activated small interfering RNAs in virus-infected Brassicaceae crops show a common host gene-silencing pattern affecting photosynthesis and stress response.The New phytologist · 2021Article
- Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Frontiers in microbiology · 2021Article
- High-Throughput Sequencing of Small RNAs for the Sanitary Certification of Viruses in Grapevine.Frontiers in plant science · 2021Article
- Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology.Frontiers in genetics · 2021Review
- siRNA biogenesis and advances in topically applied dsRNA for controlling virus infections in tomato plants.Scientific reports · 2020Article
- Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Whole-Genome Deep Sequencing Reveals Host-DrivenInternational journal of molecular sciences · 2020Article
- Review
- Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine (Frontiers in microbiology · 2020Article
- Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves.Scientific reports · 2019Article
- Analyses of virus/viroid communities in nectarine trees by next-generation sequencing and insight into viral synergisms implication in host disease symptoms.Scientific reports · 2019Article
- Article
- Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics.Viruses · 2019Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Virus-infected plants accumulate abundant, 21-24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this 'siRNA omics' approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.
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