Detection of RNA viruses in tomato crops from eastern Antioquia (Colombia) using next-generation sequencing (NGS)
Keywords:
Carlavirus, Potexvirus, RT-PCR, sequencing, Solanum lycopersicumAbstract
Viral diseases are one of the most important limiting factors of the production of tomato. In the world about 136 viral species have been reported to infect this plant but only 15 have been registered in Colombia, thus far. The latter suggests that the tomato virome in Colombia is underrepresented. In this work, the diversity of RNA viruses infecting tomato var. Chonto crops in eastern Antioquia was evaluated by RT-PCR, RT-qPCR, Next-generation sequencing (NGS) and Sanger sequencing. NGS revealed the presence of Potato virus Y (PVY), Potato yellow vein virus (PYVV), Potato virus S (PVS) and Potato virus X (PVX). PVX (6428 nt) and PVS (8492 nt) were the most abundant viruses and were completely assembled using the RNA-seq data. Infection by all four viruses was confirmed by RT-qPCR and Sanger sequencing of RT-PCR amplicons. These results highlight the need to strengthen the integrated disease management program for tomato in Colombia. This work is the first formal report of PVS and PVX naturally infecting tomato in Colombia.
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References
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25. Muñoz, L., P.A. Gutiérrez y M. Marín. 2017. Secuenciación del genoma completo del Potato yellow vein virus (PYVV) en tomate (Solanum lycopersicum) en Colombia. Acta Biológica Colombiana 22(1): 5-17.
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27. Nie, X. y R.P. Singh. 2001. A novel usage of random primers for multiplex RT-PCR detection of virus and viroid in aphids, leaves, and tubers. Journal of Virological Methods 91(1): 37-49.
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29. Padmanabhan, C., Y. Zheng, R. Li, Z. Fei y K. Ling. 2015. Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh. Genome Announcements 3(6): e01522-15.
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31. Predajna, L., K. Šoltys, J. Kraic, D. Mihálik y M. Glasa. 2017. First report of Potato virus S infecting tomato in Slovakia. Journal of Plant Pathology 99(3): 811.
32. Riascos, M., P.A. Gutiérrez y M.A. Marín. 2018. Identificación molecular de Potyvirus infectando cultivos de papa en el oriente de Antioquia (Colombia). Acta Biológica Colombiana 23(1): 39-50.
33. Roossinck, M.J., D.P. Martin y P. Roumagnac. 2015. Plant virus metagenomics: Advances in virus discovery. Phytopathology 105(6): 716-727.
34. Santillan, F.W, C. Fribourg, I.P. Adams, A.J. Gibbs, N. Boonham, M.A. Kehoe, S. Maina y R.A.C. Jones. 2018. The biology and phylogenetics of Potato virus S isolates from the andean region of South America. Plant Disease 102(5): 869-885.
35. Saqibab, M., S.J. Wylieb y M.G.K. Jones. 2015. Serendipitous identification of a new Iflavirus-like virus infecting tomato and its subsequent characterization. Plant Pathology 64(3): 519-527.
36. Sierra Mejía, A., Y. Gallo García, M. Estrada Arteaga, P.A. Gutiérrez y M. Marín Montoya. 2020. Detección molecular de seis virus de ARN en brotes de tubérculos de papa criolla (Solanum phureja) en Antioquia, Colombia. Bioagro 32(1): 3-14.
37. Singh, M., R.P. Singh, M.S. Fageria, X. Nie, R. Coffin y G. Hawkins. 2013. Optimization of a Real-Time RT-PCR assay and its comparison with ELISA, conventional RT-PCR and the grow-out test for large scale diagnosis of Potato virus Y in dormant potato tubers. American Journal of Potato Research 90(1): 43-50.
38. Tamayo, P. y P. Jaramillo. 2013. Enfermedades del tomate, pimentón, ají y berenjena en Colombia guía para su diagnóstico y manejo. Corpoica, Rionegro. 162 p.
39. Tamura, K., G. Stecher, D. Peterson, A. Filipski y S. Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis. Molecular Biology and Evolution 30: 2725-2729.
40. Vaca-Vaca, J.C., J.F. Betancur-Pérez y K. López-López. 2012. Distribución y diversidad genética de Begomovirus que infectan tomate (Solanum lycopersicum L.) en Colombia. Revista Colombiana de Biotecnología 14(1): 60-76.
41. Vallejo, D., P.A. Gutiérrez y M. Marín. 2016. Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk. Agronomía Colombiana 34(1): 51-60.
42. Wu, Q., S. Ding, Y. Zhang y S. Zhu. 2015. Identification of viruses and viroids by Next-Generation Sequencing and homology dependent and homology independent algorithms. Annual Review of Phytopathology 53: 1-20.
43. Xu, C., X. Sun, A. Taylor, C. Jiao, Y. Xu, X. Cai et al. 2017. Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing. Journal of Virology 91(11): e00173-17.
2. Agindotan, B.O., P.J. Shiel y P.H. Berger. 2007. Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR. Journal of Virological Methods 142(1-2): 1-9.
3. Álvarez, D., P. Gutiérrez y M. Marín. 2017. Secuenciación del genoma del Potato yellow vein virus (PYVV) y desarrollo de una prueba molecular para su detección. Bioagro 29(1): 3-14.
4. Antignus, Y. 2003. Tomato. In: G. Loebenstein y G. Thottappilly (eds.). Virus and virus-like diseases of major crops in developing countries. Kluwer Academic Publishers. Londres. 800 p.
5. Arli-Sokmen, M. y M.A. Sevİk. 2006. Viruses infecting field-grown tomatoes in Samsun province, Turkey. Archives of Phytopathology and Plant Protection 39(4): 283-288.
6. Cox, B.A. y R.A.C. Jones. 2010. Genetic variability in the coat protein gene of Potato virus S isolates and distinguishing its biologically distinct strains. Archives of Virology 155(7): 1163-1169.
7. Cueto, A.I., F. Aparisi, M.A. Achón, V. Pallás, M.A. Arcal, S. Lade y V. Medina. 2015. Characterization of a new spanish Potato virus X strain inducing symptoms in tomato. Journal of Plant Pathology 97(2): 369-372.
8. Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797.
9. Gil, J., J. Cotes y M. Marín. 2011. Incidencia de potyvirus y caracterización molecular de PVY en regiones productoras de papa (Solanum tuberosum L.) de Colombia. Revista Colombiana de Biotecnología 13(1): 85-93.
10. Gil, J.F., J.M. Cotes y M. Marín. 2012. Detección y caracterización molecular del virus X de la Papa (PVX) en regiones productoras de papa de Colombia. Revista Protección Vegetal 27(2): 69-76.
11. Gil, J.F., J.M. Cotes y M. Marín. 2013. Detección serológica y caracterización molecular de Potato virus S (PVS, Carlavirus) en cultivos de papa de Colombia. Revista de Biología Tropical 61(2): 565-575.
12. Gish, W. y D.J. States. 1993. Identification of protein coding regions by database similarity search. Nature Genetics 3: 266-272.
13. Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit et al. 2011. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29(7): 644-652.
14. Gutiérrez, P.A., J.F. Alzate y M. Marín. 2015. Complete genome sequence of an isolate of Potato virus X (PVX) infecting Cape gooseberry (Physalis peruviana) in Colombia. Virus Genes 50(3): 518-522.
15. Hanssen, I.M., M. Lapidot y B. Thomma. 2010. Emerging viral diseases of tomato crops. Molecular Plant-Microbe Interactions 23(5): 539-548.
16. Hajizadeh, M. y N. Sokhandan-Bashir. 2017. Population genetic analysis of Potato virus X based on the CP gene sequence. Virus Disease 28(1): 93-101.
17. Imbeaud, S., E. Graudens, V. Boulanger, X. Barlet, P. Zaborski, E. Eveno et al. 2005. Toward standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Research 33(6): e56.
18. Jones, R.C.A. 2014. Plant virus ecology and epidemiology: Historical perspectives, recent progress and future prospects. Annals of Applied Biology 164: 320-347.
19. Lin, Y.H., J.A. Abad, C.J. Maroon-Lango, K.L. Perry y H.R. Pappu. 2014. Molecular characterization of domestic and exotic Potato virus S isolates and a global analysis of genomic sequences. Archives of Virology 159(8): 2115-2122.
20. Massart, S., T. Candresse, J. Gil, C. Lacomme, L. Predajna, M. Ravnikar et al. 2017. A Framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Frontiers in Microbiology 8: 45.
21. Medina, H, P. Gutiérrez y M. Marín. 2015. Detección del Potato virus Y (PVY) en tubérculos de papa mediante TAS-ELISA y qRT-PCR en Antioquia (Colombia). Bioagro 27: 83-92.
22. Morales, F., P. Tamayo, M. Castaño, C. Olaya, A. Martínez y A. Velasco, A. 2009. Enfermedades virales del tomate (Solanum lycopersicum) en Colombia. Fitopatotología Colombiana 33: 23-27.
23. Moussa, A.B., M. Makni y M. Marrakchi, M. 2000. Identification of the principal viruses infecting tomato crops in Tunisia. Bulletin OEPP 30(2): 293-296.
24. Muñoz, L., P.A. Gutiérrez y M. Marín. 2016. Detección y secuenciación del genoma del Potato virus Y (PVY) que infecta plantas de tomate en Antioquia, Colombia. Bioagro 28(2): 69-80.
25. Muñoz, L., P.A. Gutiérrez y M. Marín. 2017. Secuenciación del genoma completo del Potato yellow vein virus (PYVV) en tomate (Solanum lycopersicum) en Colombia. Acta Biológica Colombiana 22(1): 5-17.
26. Muñoz-Escudero, D., P. Gutiérrez y M. Marín. 2016. Detection and genome characterization of Potato virus Y isolates infecting potato (Solanum tuberosum L.) in La Union (Antioquia, Colombia). Agronomía Colombiana 34(3): 317-328.
27. Nie, X. y R.P. Singh. 2001. A novel usage of random primers for multiplex RT-PCR detection of virus and viroid in aphids, leaves, and tubers. Journal of Virological Methods 91(1): 37-49.
28. Nyalugwe, E.P., C.R. Wilson, B.A. Coutts y R.A.C. Jones. 2012. Biological properties of Potato virus X in potato: effects of mixed infection with Potato virus S and resistance phenotypes in cultivars from three continents. Plant Disease 96(1): 43-54.
29. Padmanabhan, C., Y. Zheng, R. Li, Z. Fei y K. Ling. 2015. Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh. Genome Announcements 3(6): e01522-15.
30. Prasannath, K., K.N.P. Dharmadasa, D.M. De Costa y K.S. Hemachandra. 2014. Variations of incidence, types of virus diseases and insect vector populations of tomato (Solanum lycopersicum L.), grown in different agroecological regions of Sri Lanka under two crop management systems. Tropical Agricultural Research 25(3): 376-395.
31. Predajna, L., K. Šoltys, J. Kraic, D. Mihálik y M. Glasa. 2017. First report of Potato virus S infecting tomato in Slovakia. Journal of Plant Pathology 99(3): 811.
32. Riascos, M., P.A. Gutiérrez y M.A. Marín. 2018. Identificación molecular de Potyvirus infectando cultivos de papa en el oriente de Antioquia (Colombia). Acta Biológica Colombiana 23(1): 39-50.
33. Roossinck, M.J., D.P. Martin y P. Roumagnac. 2015. Plant virus metagenomics: Advances in virus discovery. Phytopathology 105(6): 716-727.
34. Santillan, F.W, C. Fribourg, I.P. Adams, A.J. Gibbs, N. Boonham, M.A. Kehoe, S. Maina y R.A.C. Jones. 2018. The biology and phylogenetics of Potato virus S isolates from the andean region of South America. Plant Disease 102(5): 869-885.
35. Saqibab, M., S.J. Wylieb y M.G.K. Jones. 2015. Serendipitous identification of a new Iflavirus-like virus infecting tomato and its subsequent characterization. Plant Pathology 64(3): 519-527.
36. Sierra Mejía, A., Y. Gallo García, M. Estrada Arteaga, P.A. Gutiérrez y M. Marín Montoya. 2020. Detección molecular de seis virus de ARN en brotes de tubérculos de papa criolla (Solanum phureja) en Antioquia, Colombia. Bioagro 32(1): 3-14.
37. Singh, M., R.P. Singh, M.S. Fageria, X. Nie, R. Coffin y G. Hawkins. 2013. Optimization of a Real-Time RT-PCR assay and its comparison with ELISA, conventional RT-PCR and the grow-out test for large scale diagnosis of Potato virus Y in dormant potato tubers. American Journal of Potato Research 90(1): 43-50.
38. Tamayo, P. y P. Jaramillo. 2013. Enfermedades del tomate, pimentón, ají y berenjena en Colombia guía para su diagnóstico y manejo. Corpoica, Rionegro. 162 p.
39. Tamura, K., G. Stecher, D. Peterson, A. Filipski y S. Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis. Molecular Biology and Evolution 30: 2725-2729.
40. Vaca-Vaca, J.C., J.F. Betancur-Pérez y K. López-López. 2012. Distribución y diversidad genética de Begomovirus que infectan tomate (Solanum lycopersicum L.) en Colombia. Revista Colombiana de Biotecnología 14(1): 60-76.
41. Vallejo, D., P.A. Gutiérrez y M. Marín. 2016. Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk. Agronomía Colombiana 34(1): 51-60.
42. Wu, Q., S. Ding, Y. Zhang y S. Zhu. 2015. Identification of viruses and viroids by Next-Generation Sequencing and homology dependent and homology independent algorithms. Annual Review of Phytopathology 53: 1-20.
43. Xu, C., X. Sun, A. Taylor, C. Jiao, Y. Xu, X. Cai et al. 2017. Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing. Journal of Virology 91(11): e00173-17.
Published
2020-10-01
How to Cite
Gallo García, Y., Muñoz Baena, L., Toro Fernández, L. F., Gutiérrez Sánchez, P. A., & Marín Montoya, M. (2020). Detection of RNA viruses in tomato crops from eastern Antioquia (Colombia) using next-generation sequencing (NGS). Bioagro, 32(3), 147-158. Retrieved from https://revistas.uclave.org/index.php/bioagro/article/view/2757
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