Abstract
Begomovirus infection was suspected in tomato plants exhibiting symptoms of curling and deformation of leaves observed in a survey conducted in northern and central Peru. Rolling circle amplification and restriction fragment length polymorphism analyses suggested that a begomovirus was present in symptomatic plants. The full-length sequence of a begomovirus DNA component was determined, comprising 2591 nucleotides. Based on its genome organization, we suggest it corresponds to the DNA-A of a New World begomovirus. Less than 89% nucleotide sequence identity to known begomoviruses was found, indicating that it corresponds to an isolate of a distinct begomovirus species for which the name tomato leaf deformation virus (ToLDeV) is proposed. Different stretches of the genomic component have the highest sequence identity with different viruses compatible with a recombinant origin. Sequence segments shared common ancestors with isolates of either soybean blistering mosaic virus, tomato yellow spot virus, or tomato chino La Paz virus. Partial sequence analysis of begomovirus isolates present in symptomatic tomato samples collected in northern and central Peru suggested widespread occurrence of this new begomovirus. This is the first confirmation of a begomovirus infection in tomatoes in Peru.
References
Argüello-Astorga, G. R., & Ruiz-Medrano, R. (2001). An iteron-related domain is associated to Motif 1 in the replication proteins of geminiviruses: identification of potential interacting amino acid-base pairs by a comparative approach. Archives of Virology, 146, 1465–1485.
Duffy, S., & Holmes, E. C. (2007). Multiple introductions of the Old World begomovirus tomato yellow leaf curl virus into the New World. Applied and Environmental Microbiology, 73, 7114–7117.
Fargette, D., Konaté, G., Fauquet, C., Muller, E., Peterschmitt, M., & Thresh, J. M. (2006). Molecular ecology and emergence of tropical plant viruses. Annual Review of Phytopathology, 44, 235–260.
Fauquet, C. M., & Stanley, J. (2005). Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Archives of Virology, 150, 2151–2179.
Fauquet, C., Briddon, R., Brown, J., Moriones, E., Stanley, J., Zerbini, M., et al. (2008). Geminivirus strain demarcation and nomenclature. Archives of Virology, 153, 783–821.
Fiallo-Olivé, E., Martínez-Zubiaur, Y., & Rivera-Bustamante, R. F. (2009). Tomato yellow leaf distortion virus, a new bipartite begomovirus infecting tomato in Cuba. Plant Pathology, 58, 785.
Fourment, M., Gibbs, A. J., & Gibbs, M. J. (2008). SWeBLAST: a sliding window web-based BLAST tool for recombinant analysis. Journal of Virological Methods, 152, 98–101.
Galvao, R. M., Mariano, A. C., Luz, D. F., Alfenas, P. F., Andrade, E. C., Zerbini, F. M., et al. (2003). A naturally occurring recombinant DNA-A of a typical bipartite begomovirus does not require the cognate DNA-B to infect Nicotiana benthamiana systemically. The Journal of General Virology, 84, 715–726.
Haible, D., Kober, S., & Jeske, H. (2006). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Journal of Virological Methods, 135, 9–16.
Idris, A. M., & Brown, J. K. (1998). Sinaloa tomato leaf curl geminivirus: biological and molecular evidence for a new subgroup III virus. Phytopathology, 88, 648–657.
Inoue-Nagata, A. K., Albuquerque, L. C., Rocha, W. B., & Nagata, T. (2004). A simple method for cloning the complete begomovirus genome using the bacteriophage Φ29 DNA polymerase. Journal of Virological Methods, 116, 209–211.
Jeske, H. (2007). Replication of geminiviruses and the use of rolling circle amplification for their diagnosis. In H. Czosnek (Ed.), Tomato yellow leaf curl virus disease management, molecular biology, breeding for resistance (pp. 141–156). Dordrecht: Springer.
Jeske, H. (2009). Geminiviruses. Current Topics in Microbiology and Immunology, 331, 185–226.
Mansoor, S., Zafar, Y., & Briddon, R. W. (2006). Geminivirus disease complexes: the threat is spreading. Trends in Plant Science, 11, 209–212.
Martin, D. P., Van der Walt, E., Posada, D., & Rybicki, E. P. (2005a). The evolutionary value of recombination is constrained by genome modularity. PLoS Genetics, 1, 475–479.
Martin, D. P., Williamson, C., & Posada, D. (2005b). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics, 21, 260–262.
Morales, F. J., & Anderson, P. K. (2001). The emergence and dissemination of whitefly-transmitted geminiviruses in Latin America. Archives of Virology, 146, 415–441.
Moriones, E., & Navas-Castillo, J. (2000). Tomato yellow leaf curl virus, an emerging virus complex causing epidemics worldwide. Virus Research, 71, 123–134.
Moriones, E., García-Andrés, S., & Navas-Castillo, J. (2007). Recombination in the TYLCV complex: a mechanism to increase genetic diversity. Implications for plant resistance development. In H. Czosnek (Ed.), Tomato yellow leaf curl virus disease management, molecular biology, breeding for resistance (pp. 119–138). Dordrecht: Springer.
Murayama, A., Aragón, L., & Fernández-Northcote, E. N. (2005). Nuevo begomovirus del grupo del nuevo mundo asociado al encrespamiento de la hoja del tomate en la costa del Perú. Fitopatología, 40, 82.
Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265, 218–225.
Rick, C. M. (1976). Tomato. In N. D. Simmonds (Ed.), The evolution of crop plants (pp. 268–273). London and New York: Longman.
Rojas, M. R., Gilbertson, R. J., Rusell, D. R., & Maxwell, D. P. (1993). Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Disease, 77, 340–347.
Rojas, M. R., Hagen, C., Lucas, W. J., & Gilbertson, R. L. (2005). Exploiting chinks in the plant’s armor: evolution and emergence of geminiviruses. Annual Review of Phytopathology, 43, 361–394.
Seal, S. E., Jeger, M. J., & van den Bosch, F. (2006). Begomovirus evolution and disease management. Advances in Virus Research, 67, 297–316.
Shepherd, D. N., Martin, D. P., Lefeuvre, P., Monjane, A. L., Owor, B. E., Rybicki, E. P., et al. (2008). A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. Journal of Virological Methods, 149, 97–102.
Stanley, J., Bisaro, D. M., Briddon, R. W., Brown, J. K., Fauquet, C. M., Harrison, B. D., et al. (2005). Geminiviridae. In C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger, & L. A. Ball (Eds.), Virus taxonomy, VIIIth Report of the International Committee on taxonomy of viruses (pp. 301–326). London: Elsevier/Academic Press.
van der Walt, E., Rybicki, E. P., Varsani, A., Polston, J. E., Billharz, R., Donaldson, L., et al. (2009). Rapid host adaptation by extensive recombination. The Journal of General Virology, 90, 734–746.
Varma, A., & Malathi, V. G. (2003). Emerging geminivirus problems: a serious threat to crop production. The Annals of Applied Biology, 142, 145–164.
Zhou, X. P., Xie, Y., & Zhang, Z. K. (2001). Molecular characterization of a distinct begomovirus infecting tobacco in Yunnan, China. Archives of Virology, 146, 1599–1606.
Acknowledgements
This work was supported through grant GEN2006-27770-C2-2 (Ministerio de Educación y Ciencia, Spain, co-financed by FEDER) in the frame of the ERA-NET Plant Genomics project ERA-PG 040B “RCA-GENOMICS” of the European Commission 6th Framework Programme for research and the Trilateral Cooperation GABI-GENOPLANTE-MEC. B. Márquez contract was financed by this same project. E. Fiallo-Olivé was supported by a MAEC-AECID fellowship from Ministerio de Asuntos Exteriores y de Cooperación, Spain. We thank S. García-Andrés for preliminar analyses, and M. V. Martín, R Tovar, and R. Campos for technical assistance.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Márquez-Martín, B., Aragón-Caballero, L., Fiallo-Olivé, E. et al. Tomato leaf deformation virus, a novel begomovirus associated with a severe disease of tomato in Peru. Eur J Plant Pathol 129, 1–7 (2011). https://doi.org/10.1007/s10658-010-9699-5
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-010-9699-5