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Detection of Plant Viruses in Natural Environments by Using RNA-Seq

Part of the Methods in Molecular Biology book series (MIMB,volume 1236)

Abstract

Sequencing of RNA by next generation sequencers, RNA-Seq, is revolutionizing virus detection. In addition to the unbiased detection of various viruses from wild plants in natural environments, RNA-Seq also allows for the parallel collection of host plant transcriptome data. Host transcriptome data are highly valuable for studying the responses of hosts to viral infections, as well as viral host manipulation. When detecting viruses using RNA-Seq, it is critical to choose appropriate methods for the removal of rRNA from total RNA. Although viruses with polyadenylated genomes can be detected by RNA-Seq following mRNA purification using oligo-dT beads, viruses with non-polyadenylated genomes are not effectively detected. However, such viruses can be detected by RNA-Seq using the rRNA selective depression method. The high-throughput and cost-effective method of RNA-Seq library preparation which is described here allows us to detect a broad range of viruses in wild plants.

Key words

  • Virus detection
  • RNA-Seq
  • Wild plant
  • Selective depression of rRNA
  • Natural environment

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Acknowledgement

This work was supported by JST PRESTO (to A.J.N.) and the Next Program (GS013) (to H.K.).

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Correspondence to Atsushi J. Nagano or Hiroshi Kudoh .

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Nagano, A.J., Honjo, M.N., Mihara, M., Sato, M., Kudoh, H. (2015). Detection of Plant Viruses in Natural Environments by Using RNA-Seq. In: Uyeda, I., Masuta, C. (eds) Plant Virology Protocols. Methods in Molecular Biology, vol 1236. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1743-3_8

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  • DOI: https://doi.org/10.1007/978-1-4939-1743-3_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1742-6

  • Online ISBN: 978-1-4939-1743-3

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