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Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses

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Abstract

In a virus-infected plant, small interfering RNAs (siRNAs) corresponding to the viral genome form a large proportion of the small RNA population. It is possible to reassemble significant portions of the virus sequence from overlapping siRNA sequences and use these to identify the virus. We tested this technique with a resistance-breaking and a non-resistance-breaking strain of tomato spotted wilt virus (TSWV). We were able to assemble contigs covering 99% of the genomes of both viruses. The abundance of TSWV siRNAs allowed us to detect TSWV at early time points before the onset of symptoms, at levels too low for conventional detection. Combining traditional and bioinformatic detection methods, we also measured how replication of the resistance-breaking strain differed from the non-resistance-breaking strain in susceptible and resistant tomato varieties. We repeated this technique in identification of a squash-infecting geminivirus and also used it to identify an unspecified tospovirus.

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Authors and Affiliations

  1. Monsanto Company, Calgene Campus, Davis, CA, USA

    Charles Hagen, Alessandra Frizzi & Shihshieh Huang

  2. Monsanto Vegetable Seeds, Woodland, CA, USA

    John Kao & Lijie Jia

  3. Monsanto Company, Creve Coeur, St. Louis, MO, USA

    Mingya Huang & Yuanji Zhang

Authors
  1. Charles Hagen
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  2. Alessandra Frizzi
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  3. John Kao
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  4. Lijie Jia
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  5. Mingya Huang
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  6. Yuanji Zhang
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  7. Shihshieh Huang
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Corresponding author

Correspondence to Charles Hagen.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resources 1-4 Viral genomes assembled from siRNA sequences. In all cases, bases confirmed by siRNA contigs are in capital letters (i.e., A, G, C, T); gaps filled in with a template are in lower case (i.e., a, g, c, t).

Online Resource 1: RB-TSWV genome (TXT 16.2 kb)

Online Resource 2: TSWV genome (TXT 5.10 kb)

Online Resource 3: SLCV genome (TXT 16.2 kb)

Online Resource 4: CaCV genome (TXT 16.8 kb)

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Hagen, C., Frizzi, A., Kao, J. et al. Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses. Arch Virol 156, 1209–1216 (2011). https://doi.org/10.1007/s00705-011-0979-y

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  • DOI: https://doi.org/10.1007/s00705-011-0979-y

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