Archives of Virology

, Volume 163, Issue 7, pp 1863–1875 | Cite as

Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus

  • Yonatan Maayan
  • Eswari P. J. Pandaranayaka
  • Dhruv Aditya Srivastava
  • Moshe Lapidot
  • Ilan Levin
  • Aviv Dombrovsky
  • Arye Harel
Original Article


In September 2014, a new tobamovirus was discovered in Israel that was able to break Tm-2-mediated resistance in tomato that had lasted 55 years. The virus was isolated, and sequencing of its genome showed it to be tomato brown rugose fruit virus (ToBRFV), a new tobamovirus recently identified in Jordan. Previous studies on mutant viruses that cause resistance breaking, including Tm-2-mediated resistance, demonstrated that this phenotype had resulted from only a few mutations. Identification of important residues in resistance breakers is hindered by significant background variation, with 9–15% variability in the genomic sequences of known isolates. To understand the evolutionary path leading to the emergence of this resistance breaker, we performed a comprehensive phylogenetic analysis and genomic comparison of different tobamoviruses, followed by molecular modeling of the viral helicase. The phylogenetic location of the resistance-breaking genes was found to be among host-shifting clades, and this, together with the observation of a relatively low mutation rate, suggests that a host shift contributed to the emergence of this new virus. Our comparative genomic analysis identified twelve potential resistance-breaking mutations in the viral movement protein (MP), the primary target of the related Tm-2 resistance, and nine in its replicase. Finally, molecular modeling of the helicase enabled the identification of three additional potential resistance-breaking mutations.



This research was supported by a grant from the Israeli Chief Scientist, Ministry of Agriculture (grant number 20-10-0070).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

Not applicable.

Supplementary material

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Supplementary material 1 (PDF 803 kb)
705_2018_3819_MOESM2_ESM.doc (34 kb)
Supplementary material 2 (DOC 34 kb)


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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Yonatan Maayan
    • 1
  • Eswari P. J. Pandaranayaka
    • 1
  • Dhruv Aditya Srivastava
    • 1
  • Moshe Lapidot
    • 1
  • Ilan Levin
    • 1
  • Aviv Dombrovsky
    • 2
  • Arye Harel
    • 1
  1. 1.Department of Vegetable and Field Crop Research, Institute of Plant SciencesAgricultural Research Organization, Volcani CenterRishon LeZionIsrael
  2. 2.Department of Plant Pathology and Weed Research, Institute of Plant ProtectionAgricultural Research Organization, Volcani CenterRishon LeZionIsrael

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