Microbial Ecology

, Volume 78, Issue 1, pp 113–121 | Cite as

A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq

  • Mari KamitaniEmail author
  • Atsushi J. Nagano
  • Mie N. Honjo
  • Hiroshi KudohEmail author
Plant Microbe Interactions


Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.


Asymptomatic infection Brassicaceae Plant communities Plant viruses RNA-Seq Viral ecology 



We would like to thank Dr. Y. Sato for his helpful comments on statistical analysis.


This work was supported by KAKENHI (JP26221106, 16H06171, JP16H01473), CREST (JPMJCR15O1, JPMJCR15O2), and Grant-in-Aid for JSPS Fellows (15J00628).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

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ESM 1 (PDF 4389 kb)
248_2018_1271_MOESM2_ESM.docx (35 kb)
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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center for Ecological ResearchKyoto UniversityShigaJapan
  2. 2.Faculty of AgricultureRyukoku UniversityShigaJapan

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