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.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Genome, Viral*; DNA, Circular/*chemistry ; DNA, Viral/*chemistry ; Geminiviridae/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Plants, Genetically Modified/*virology ; Sequence Analysis, DNA/*methods; Algorithms ; Plants, Genetically Modified/genetics ; RNA Interference

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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0 (DNA, Circular)
0 (DNA, Viral)

Date Created: 20181026 Date Completed: 20190820 Latest Revision: 20200309

20240829

PMC6344846

10.1093/nar/gky914

30357413