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Exploring the virome of Vasconcellea x heilbornii: the first step towards a sustainable production program for babaco in Ecuador

Abstract

The virome of babaco (Vasconcellea x heilbornii) —a non-traditional fruit crop native to Ecuador— was investigated by high-throughput sequencing (HTS) on plants obtained from a commercial nursery. Six virus-like sequences were detected, including the full length of papaya ringspot virus (PRSV) and an RNA-dependent-RNA-polymerase (RdRp) sequence with homology to papaya virus Q. Three RNA sequences were found with homology, respectively, to apple latent spherical virus (genus Cheravirus, 71% nt identity), cherry leaf roll virus (genus Nepovirus, 54% nt identity) and Citrullus lanatus cryptic virus (genus Deltapartitivirus, 66% nt identity); whereas a DNA pararetrovirus-like sequence with homology to citrus endogenous pararetrovirus (58% nt identity) was also detected. RT-PCR-based virus surveys on a total of 284 samples collected from three provinces revealed that the partitivirus- and pararetrovirus-like sequences were present in 100% of tested plants; whereas the other virus sequences were detected in up to 68% of plants and were associated with different symptoms. This work provides information on the occurrence and prevalence of PRSV and five additional virus-like sequences in babaco, a vegetatively propagated crop, supporting the need for a virus-free certification program.

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References

  1. Adams, M. J., Lefkowitz, E. J., King, A. M. Q., Bamford, D. H., Breitbart, M., Davison, A. J., Ghabrial, S. A., Gorbalenya, A. E., Knowles, N. J., Krell, P., Lavigne, R., Prangishvili, D., Sanfaçon, H., Siddell, S. G., Simmonds, P., & Carstens, E. B. (2015). Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses (2015). Archives of Virology, 160, 1837–1850. https://doi.org/10.1007/s00705-015-2425-z.

    CAS  Article  PubMed  Google Scholar 

  2. Adams, I., & Fox, A. (2016). Diagnosis of plant viruses using next-generation sequencing and metagenomic analysis. In A. Wang & X. Zhou (Eds.), Current research topics in plant virology (pp. 323–335). Cham: Springer International Publishing.

    Chapter  Google Scholar 

  3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410.

    CAS  Article  Google Scholar 

  4. Alvarez-Quinto, R. A., Cornejo-Franco, J. F., & Quito-Avila, D. F. (2017). Characterization of a not so new potexvirus from babaco (Vasconcellea x heilbornii). PLoS One, 12(12), e0189519.

    Article  Google Scholar 

  5. Cornejo-Franco, J. F., Alvarez-Quinto, R. A., & Quito-Avila, D. F. (2018). Transmission of the umbra-like papaya virus Q in Ecuador and its association with meleira-related viruses from Brazil. Crop Protection, 110, 99–102.

    Article  Google Scholar 

  6. Fuentes, G., & Santamaría, J. M. (2014). Papaya (Carica papaya L.): Origin, domestication, and production. In R. Ming & P. H. Moore (Eds.), Genetics and genomics of papaya (pp. 3–15). Springer New York: New York, NY.

    Chapter  Google Scholar 

  7. Halgren, A., Tzanetakis, I. E., & Martin, R. R. (2007). Identification, characterization, and detection of black raspberry necrosis virus. Phytopathology, 97(1), 44–50.

    CAS  Article  Google Scholar 

  8. Hull, R., Harper, G., & Lockhart, B. (2000). Viral sequences integrated into plant genomes. Trends in Plant Science, 5, 362–365.

    CAS  Article  Google Scholar 

  9. Kyndt, T., Romeijn-Peeters, E., Van Droogenbroeck, B., Romero-Motochi, J. P., Gheysen, G., & Goetghebeur, P. (2005). Species relationships in the genus Vasconcellea (Caricaceae) based on molecular and morphological evidence. American Journal of Botany, 92(6), 1033–1044.

    CAS  Article  Google Scholar 

  10. Nibert, M. L., Ghabrial, S. A., Maiss, E., Lesker, T., Vainio, E. J., Jiang, D. H., & Suzuki, N. (2014). Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Research, 188, 128–141.

    CAS  Article  Google Scholar 

  11. Quito-Avila, D. F., Alvarez, R. A., Ibarra, M. A., & Martin, R. R. (2015). Detection and partial genome sequence of a new umbra-like virus of papaya discovered in Ecuador. European Journal of Plant Pathology, 143(1), 199–204.

    Article  Google Scholar 

  12. Robles-Carrión, A. R., Herrera Isla, L., & Torres, G. R. (2016). El babaco (Vasconcellea heilbornii var. pentagona Badillo). Principales agentes fitopatógenos y estrategias de control. Centro Agrícola, 43, 83–92.

    Google Scholar 

  13. Ryabov, E. V., Taliansky, M. E., Robinson, D. J., Waterhouse, P. M., Murant, A. F., de Zoeten, G. A., Falk, B. W., Vetten, H. J., & Gibbs, M. J. (2012). Genus Umbravirus. In A. King, M. J. Adams, E. C. Carstens, & E. J. Lefkowitz (Eds.), Virus taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses (pp. 1191–1195). New York: Elsevier.

    Google Scholar 

  14. Sá Antunes, T. F., Amaral, R. J., Ventura, J. A., Godinho, M. T., Amaral, J. G., Souza, F. O., et al. (2016). The dsRNA virus papaya Meleira virus and an ssRNA virus are associated with papaya sticky disease. PLoS One, 11(5), e0155240.

    Article  Google Scholar 

  15. Scheldeman, X., Willemen, L., Coppens d’Eeckenbrugge, G., Romeijn-Peeters, E., Restrepo, M. T., Romero Motoche, J., et al. (2007). Distribution, diversity and environmental adaptation of highland papayas (Vasconcellea spp.) in tropical and subtropical America. In D. L. Hawksworth & A. T. Bull (Eds.), Plant conservation and biodiversity (pp. 293–310). Dordrecht: Springer Netherlands.

    Google Scholar 

  16. Thompson, J. R., Dasgupta, I., Fuchs, M., Iwanami, T., Karasev, A. V., Petrzik, K., Sanfaçon, H., Tzanetakis, I., Van der Vlugt, R., Wetzel, T., Yoshikawa, N., Lefkowitz, E. J., Davison, A. J., Siddell, S. G., Simmonds, P., Adams, M. J., Smith, D. B., Orton, R. J., & Knowles, N. J. (2017). ICTV virus taxonomy profile: Secoviridae. The Journal of General Virology, 98, 529–531.

    CAS  Article  Google Scholar 

  17. Villamor, D. E. V., Ho, T., Al Rwahnih, M., Martin, R. R., & Tzanetakis, I. E. (2019). High throughput sequencing for plant virus detection and discovery. Phytopathology, 109(5), 716–725.

    CAS  Article  Google Scholar 

  18. Xin, M., Cao, M., Liu, W., Ren, Y., Lu, C., & Wang, X. (2017). The genomic and biological characterization of Citrullus lanatus cryptic virus infecting watermelon in China. Virus Research, 232, 106–112.

    CAS  Article  Google Scholar 

  19. Yu, H., Wang, X., Lu, Z., Xu, Y., Deng, X., & Xu, Q. (2019). Endogenous pararetrovirus sequences are widely present in Citrinae genomes. Virus Research, 262, 48–53.

    CAS  Article  Google Scholar 

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Acknowledgements

The authors thank Dr. Ricardo Oliva for funding HTS; the Ecuadorean University Network (REDU), through ESPOL, for additional funding; babaco growers in the selected areas for granting access to their orchards or nurseries; and Dr. Gary Kinard for critical review of the manuscript. This work was conducted under Genetic Resource Access Permit # MAE–DNB–CM–2018–0098 granted by the Department of Biodiversity of the Ecuadorean Ministry of the Environment.

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Correspondence to Diego F. Quito-Avila.

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Cornejo-Franco, J.F., Medina-Salguero, A., Flores, F. et al. Exploring the virome of Vasconcellea x heilbornii: the first step towards a sustainable production program for babaco in Ecuador. Eur J Plant Pathol 157, 961–968 (2020). https://doi.org/10.1007/s10658-020-02037-2

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Keywords

  • Vasconcellea x heilbornii
  • Virus
  • Babaco
  • Papaya
  • Ecuador