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Diversity of Citrus tristeza virus populations in commercial grapefruit orchards in Southern Africa, determined using Illumina MiSeq technology

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Abstract

Grapefruit cultivars are highly sensitive to CTV infections and in order to increase their productive lifespan, the Southern African citrus industry makes use of cross-protection. However, the breakdown of cross-protection is commonly observed in commercial grapefruit plantings. In order to determine which genotypes of CTV are associated with commercial Citrus x paradisi (Macfad.) cv. ‘Star Ruby’ in Southern Africa, 192 samples, pre-immunised with the GFMS 12 population, were collected from the grapefruit production areas of Hoedspruit, Malelane, Swaziland, Northern Cape, Sundays River Valley and Nkwalini Valley and six samples from non-pre-immunised plants in Letsitele as well as three samples from greenhouse maintained plants harbouring populations derived from the original GFMS 12 source. The p33 gene was amplified with direct Sanger sequencing performed on the resulting amplicons. A subset of 92 samples randomly selected and p33 gene amplicons subjected to Illumina MiSeq amplicon sequencing. High levels of CTV diversity were observed between and within orchards. Most populations were made up of a dominant component with several minor sequence types. Resistance Breaking (RB) sequences were most numerous, especially in recently planted orchards and present within all of the populations. The Kpg3/SP/T3 group appeared to be the second most prevalent, with increased prevalence in older orchards. Sequences mapping to HA 16–5, VT, AT-1, T36, Taiwan-Pum/M/T5 and T30, were represented sporadically within numerous collection sites.

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References

  • Albiach, M. R., da Graça, J. V., van Vuuren, S. P., Guerri, J., Cambra, M., Laigret, F., & Moreno, P. (1996). The effects of different hosts and natural disease pressure on molecular profiles of mild isolates of citrus tristeza virus (CTV). In: proc. In 13th Conf. IOCV. IOCV, riverside, California (pp. 147–153).

    Google Scholar 

  • Atallah, O. O., Kang, S. H., El-Mohtar, C. A., Shilts, T., Bergua, M., & Folimonova, S. Y. (2016). A 5′-proximal region of the Citrus tristeza virus genome encoding two leader proteases is involved in virus superinfection exclusion. Virology, 489, 108–115.

    Article  CAS  PubMed  Google Scholar 

  • Bar-Joseph, M., Marcus, R., & Lee, R. F. (1989). The continuous challenge of citrus tristeza virus control. Annual Review of Phytopathology, 27, 291–316.

    Article  Google Scholar 

  • Bergua, M., Zwart, M. P., El-Mohtar, C., Shilts, T., Elena, S. F., & Folimonova, S. Y. (2016). A viral protein mediates superinfection exclusion at the whole-organism level but is not required for exclusion at the cellular level. Journal of Virology, 88, 11327–11338.

    Article  Google Scholar 

  • da Graça, J. V., Marias, L. J., & von Broemsen, L. A. (1984). Severe tristeza stem pitting decline of young grapefruit in South Africa. In: proc. 9th Conf (pp. 62–65). Riverside, California: IOCV. IOCV.

    Google Scholar 

  • Folimonova, S. Y. (2012). Superinfection exclusion is an active virus-controlled function that requires a specific viral protein. Journal of Virology, 86, 5554–5561.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Folimonova, S. Y. (2013). Developing an understanding of cross-protection by Citrus tristeza virus. Frontiers in Microbiology, 4, e76.

    Article  Google Scholar 

  • Folimonova, S. Y., Robertson, C. J., Shilts, T., Folimonov, A. S., Hilf, M. E., Garnsey, S. M., & Dawson, W. O. (2010). Infection with strains of Citrus Tristeza Virus does not exclude superinfection by other strains of the virus. Journal of Virology, 84, 1314–1325.

    Article  CAS  PubMed  Google Scholar 

  • Gal-On, A., & Shiboleth, Y. M. (2005). Cross-protection. In G. Loebenstein & J. P. Carr (Eds.), Natural resistance mechanisms of plants to viruses (pp. 261–288). The Netherlands: Springer, Dordrecht.

    Google Scholar 

  • Garnsey, S. M., Civerolo, E. L., Gumpf, D. J., Paul, C., Hilf, M. E., Lee, R. F., Brlansky, R. H., Yokomi, R. K., & Hartung, J. S. (2005). Biological characterization of an international collection of citrus tristeza virus (CTV) isolates. In Proc 16th Conf. IOCV (pp. 75–93). Riverside, California, United States: IOCV.

    Google Scholar 

  • Gottwald, T. R., Garnsey, S. M., Cambra., M., Moreno, P., Irey, M., & Borbón, J. (1996). Differential effects of Toxoptera citricida vs. Aphis gossypii on temporal increase and spatial patterns of spread of citrus tristeza. In: proc. 13th Conf (pp. 120–129). Riverside, California: IOCV. IOCV.

    Google Scholar 

  • Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

    CAS  Google Scholar 

  • Harper, S. J. (2013). Citrus tristeza virus: evolution of complex and varied genotypic groups. Frontiers in Microbiology, 4, e93.

    Article  Google Scholar 

  • Harper S. J., Cowell S. J. & Dawson W. O. (2015). Finding balance: virus populations reach equilibrium during the infection process. Virology 485, 205–212.

  • Karasev, A. V., Boyko, V. P., Gowda, S., Nikolaeva, O. V., Hilf, M. E., Koonin, E. V., Niblett, C. L., Cline, K., Gumpf, D. J., Lee, R. F., Garnsey, S. M., Lewandowski, D. J., & Dawson, W. O. (1995). Complete sequence of the citrus tristeza virus RNA genome. Virology, 208, 511–520.

    Article  CAS  PubMed  Google Scholar 

  • Kircher, M., Sawyer, S., & Meyer, M. (2012). Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research, 40, e3.

    Article  CAS  PubMed  Google Scholar 

  • Luttig, M., van Vuuren, S. P., & van der Vyver, J. B. (2002). Differentiation of single aphid cultured sub-isolates of two south African Citrus tristeza virus isolates from grapefruit by single-strand conformation polymorphism. In: proc 15th Conf (pp. 186–196). IOCV, Riverside, California: IOCV.

    Google Scholar 

  • McClean, A. P. D. (1975). Tristeza virus complex: It’s transmission by the aphid Toxoptera citricidus. Phytophylactica, 7, 109–114.

    Google Scholar 

  • Moreno, P., Ambrόs, S., Albiach-Marti, M. R., Guerri, J., & Peña, L. (2008). Citrus tristeza virus: a pathogen that changed the course of the citrus industry. Molecular Plant Pathology, 9, 251–268.

    Article  CAS  PubMed  Google Scholar 

  • Niblett, C. L., Genc, H., Cevik, B., Halbert, S., Brown, L., Nolasco, G., Bonacalza, B., Manjunath, K. L., Febres, V. J., Pappu, H. R., & Lee, R. F. (2000). Progress on strain differentiation of Citrus tristeza virus and its application to the epidemiology of citrus tristeza disease. Virus Research, 71, 97–106.

    Article  CAS  PubMed  Google Scholar 

  • Oberholzer, P.C., Mathews, I., & Stiemie, S.F., (1949). The decline of grapefruit trees in South Africa. A preliminary report on so-called “Stem-Pitting”. Science. Bulletin Department of Agriculture South Africa, 287, 17.

  • Read, D. A., & Pietersen, G. (2015). Genotypic diversity of citrus tristeza virus within red grapefruit, in a field trial site in South Africa. European Journal of Plant Pathology, 142, 531–545.

    Article  Google Scholar 

  • Read, D. A., & Pietersen, G. (2016). PCR bias associated with conserved primer binding sites, used todetermine genotype diversity within Citrus tristeza virus populations. Journal of Virological Methods, 237, 107–113.

    Article  CAS  PubMed  Google Scholar 

  • Sambrook, J. (2001). Molecular cloning: ‘a laboratory manual’. Cold Spring Harbor laboratory press. New York: Cold Spring Harbor.

    Google Scholar 

  • Scott, K. A., Hlela, Q., Zablocki, O., Read, D., van Vuuren, S., & Pietersen, G. (2012). Genotype composition of populations of grapefruit-cross-protecting citrus tristeza virus strain GFMS12 in different host plants and aphid-transmitted sub-isolates. Archives of Virology, 158, 27–37.

    Article  PubMed  Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teixeira, D.C., Lopes, S.A., Yamamoto, P.T., Eveillard, S., Martins, E.C., de Jesus Junior, W.C., Bassanezi, R.B., Ayres, A.J., Danet, J.L., Saillard, C., & Bové, J.M. (2005). PCR detection of the two Liberibacter species associated with citrus Huanglongbing in São Paulo State, Brazil. In: Proc. 16th Conf. IOCV. IOCV, Riverside, CA. 432–438.

  • van Vuuren, S. P., Collins, R. P., & da Graça, J. V. (1993). Evaluation of citrus tristeza virus isolates for cross protection of grapefruit in South Africa. Plant Disease, 77, 24–28.

    Article  Google Scholar 

  • van Vuuren, S. P., van der Vyver, J. B., & Luttig, M. (2000). Diversity among sub-isolates of cross-protecting citrus tristeza virus isolates in South Africa. In: proc. 14th Conf (pp. 103–110). Riverside: IOCV. IOCV.

    Google Scholar 

  • van Vuuren, S. P., & Manicom, B. Q. (2005). The response of star ruby grapefruit to different Citrus tristeza virus isolates. In: proc 16th Conf (pp. 112–116). Riverside: IOCV. IOCV.

    Google Scholar 

  • von Broembsen, L. A., & Lee, A. T. C. (1988). South Africa's citrus improvement program. In: proc. 10th Conf (pp. 407–416). Riverside: IOCV. IOCV.

    Google Scholar 

  • Yoon, J. Y., Ahn, H. I., Kim, M., Tsuda, S., & Ryu, K. I. (2006). Pepper mild mottle virus pathogenicity determinants and cross protection effect of attenuated mutants in pepper. Virus Research, 118, 23–30.

    Article  CAS  PubMed  Google Scholar 

  • Zablocki, O., & Pietersen, G. (2014). Characterization of a novel citrus tristeza virus genotypewithin three cross-protecting source GFMS12 sub-isolates in South Africa by means of Illumina sequencing. Archives of Virology, 158, 2133–2139.

    Article  Google Scholar 

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Acknowledgments

We gratefully acknowledge funding from Citrus Research International (CRI), Agricultural Research Council - Plant Protection Research Institute (ARC-PPRI) and the National Research Foundation (NRF) - Technology and Human Resources for Industry Programme (THRIP) program. We also acknowledge the numerous producers that allowed samples to be collected from their orchards.

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Authors and Affiliations

  1. Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa

    D. A. Read & G. Pietersen

  2. Agricultural Research Council—Plant Protection Research Institute, Pretoria, 0186, South Africa

    G. Pietersen

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  1. D. A. Read
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  2. G. Pietersen
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Correspondence to G. Pietersen.

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Read, D.A., Pietersen, G. Diversity of Citrus tristeza virus populations in commercial grapefruit orchards in Southern Africa, determined using Illumina MiSeq technology. Eur J Plant Pathol 148, 379–391 (2017). https://doi.org/10.1007/s10658-016-1096-2

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  • DOI: https://doi.org/10.1007/s10658-016-1096-2

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