ArticleJournal of molecular biology2012
Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing.
Article in Journal of molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- ViReMaShiny: an interactive application for analysis of viral recombination data.Bioinformatics (Oxford, England) · 2022Article
- Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa.Nucleic acids research · 2022Article
- Defective Interfering Particles of Negative-Strand RNA Viruses.Trends in microbiology · 2020Review
- Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.Virus genes · 2018Article
- Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants.PLoS pathogens · 2017Article
- Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus.PLoS pathogens · 2017Article
- CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.Methods (San Diego, Calif.) · 2015Article
- ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs.Journal of molecular biology · 2015Article
- Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population.Journal of virology · 2015Article
- Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data.Nucleic acids research · 2014Article
- Confessions of an icosahedral virus crystallographer.Microscopy (Oxford, England) · 2013Review
- Article
- Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives.Frontiers in plant science · 2013Article
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Authors and funding
3 authors.
Funding
Abstract
Next-generation sequencing has been used in numerous investigations to characterize and quantify the genetic diversity of a virus sample through the mapping of polymorphisms and measurement of mutation frequencies. Next-generation sequencing has also been employed to identify recombination events occurring within the genomes of higher organisms, for example, detecting alternative RNA splicing events and oncogenic chromosomal rearrangements. Here, we combine these two approaches to profile RNA recombination within the encapsidated genome of a eukaryotic RNA virus, flock house virus. We detect hundreds of thousands of recombination events, with single-nucleotide resolution, which result in diversity in the encapsidated genome rivaling that due to mismatch mutation. We detect previously identified defective RNAs as well as many other abundant and novel defective RNAs. Our approach is exceptionally sensitive and unbiased and requires no prior knowledge beyond the virus genome sequence. RNA recombination is a powerful driving force behind the evolution and adaptation of RNA viruses. The strategy implemented here is widely applicable and provides a highly detailed description of the complex mutational landscape of the transmissible viral genome.
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