Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus
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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).
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Conflict of interest
The authors declare that they have no conflict of interest.
- 11.Craig G, Rosskopf EN, Lucas L, Mellinger HC, Adkins S (2014) First report of tomato mottle mosaic virus infecting tomato in the United States. Plant Health Progress 15:151Google Scholar
- 15.Padmanabhan CZY, Li R, Martin GB, Fei Z, Ling K-S (2015) Complete genome sequence of a tomato-Infecting tomato mottle mosaic virus in New York. Genome Announc 3:e01515–e01525Google Scholar
- 18.Webster CG, Rosskopf EN, Lucas L, Mellinger CH, Adkins S (2014) First report of Tomato mottle mosaic virus infecting tomato in the United States. Plant Health Progress 15:151–152Google Scholar
- 19.CABI (2017) Pepper mild mottle virus. https://www.cabi.org/isc/datasheet/43826
- 23.Bos L (1999) The natural selection of the chemical elements : the environment and life’s chemistry. Backhuys Publishers, LeidenGoogle Scholar
- 31.Luria N, Smith E, Reingold V, Bekelman I, Lapidot M, Levin I, Elad N, Tam Y, Sela N, Abu-Ras A, Ezra N, Haberman A, Yitzhak L, Lachman O, Dombrovsky A (2017) A New Israeli tobamovirus isolate infects tomato plants harboring Tm-22 resistance genes. PLoS One 12:e0170429CrossRefPubMedPubMedCentralGoogle Scholar
- 32.International Committee on Taxonomy of Viruses., King AMQ (2012) Virus taxonomy: classification and nomenclature of viruses: ninth report of the International Committee on Taxonomy of Viruses. Academic Press, London, Waltham, MAGoogle Scholar
- 43.Rambaut A (2014) FigTree v1.4.1. http://tree.bio.ed.ac.uk/software/figtree/
- 53.SWISS-MODEL (2018) https://swissmodel.expasy.org/docs/help
- 54.Schrodinger LLC (2015) The PyMOL Molecular Graphics System, Version 1.8. https://pymol.org/
- 75.Kobayashi M, Yamamoto-Katou A, Katou S, Hirai K, Meshi T, Ohashi Y, Mitsuhara I (2011) Identification of an amino acid residue required for differential recognition of a viral movement protein by the Tomato mosaic virus resistance gene Tm-2(2). J Plant Physiol 168:1142–1145CrossRefPubMedGoogle Scholar
- 94.Laird J, McInally C, Carr C, Doddiah S, Yates G, Chrysanthou E, Khattab A, Love AJ, Geri C, Sadanandom A, Smith BO, Kobayashi K, Milner JJ (2013) Identification of the domains of cauliflower mosaic virus protein P6 responsible for suppression of RNA silencing and salicylic acid signalling. J Gen Virol 94:2777–2789CrossRefPubMedPubMedCentralGoogle Scholar