ArticleNucleic acids research2019
A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.PLoS biology · 2025Article
- Full-Length Sequencing of Circular DNA Viruses Using CIDER-Seq.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.Frontiers in cellular and infection microbiology · 2025Article
- Review
- Review
- Viral genome sequencing methods: benefits and pitfalls of current approaches.Biochemical Society transactions · 2024Review
- Composition and Structure ofPlants (Basel, Switzerland) · 2023Article
- CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.Briefings in bioinformatics · 2022Article
- A review of strategies used to identify transposition events in plant genomes.Frontiers in plant science · 2022Review
- Differentially expressed circRNA and functional pathways in the hippocampus of epileptic mice based on next-generation sequencing.The Kaohsiung journal of medical sciences · 2021Article
- Genome editing for resistance against plant pests and pathogens.Transgenic research · 2021Review
- Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease.Biology methods & protocols · 2021Article
- Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq.Nature protocols · 2020Article
- Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses.Genome biology · 2019Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new method, CIDER-Seq (Circular DNA Enrichment sequencing) for the unbiased enrichment and long-read sequencing of viral-sized circular DNA molecules. We used CIDER-Seq to produce single-read full-length virus genomes for the first time. CIDER-Seq combines PCR-free virus enrichment with Single Molecule Real Time sequencing and a new sequence de-concatenation algorithm. We apply our technique to produce >1200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral double-stranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our method and its application in an economically important crop plant opens new possibilities in periodic virus sequence surveillance and accurate profiling of diverse circular DNA elements.
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