Advertisement

Journal of General Plant Pathology

, Volume 83, Issue 6, pp 382–389 | Cite as

Biological indexing and genetic analysis of Citrus tristeza virus in Pakistan

  • Sagheer Atta
  • Mengji Cao
  • Ummad ud din Umar
  • Yan Zhou
  • Fangyun Yang
  • Changyong ZhouEmail author
Viral and Viroid Diseases

Abstract

Citrus tristeza virus (CTV) is one of the major threats to production and fruit quality of citrus worldwide. In Pakistan, more than 95% of the citrus trees are grown on sour orange rootstock, which is highly susceptible to CTV. We studied the genetic variability of four genomic regions (p18, p20, p23 and p25) of CTV isolates collected from the citrus orchards. High divergence was revealed among the isolates from Pakistan and also with reference isolates. An inter-isolate identity range of 92.1–99.4% at the nucleotide level and 92.3–98.8% at the amino acid level was found. Phylogenetic analysis of the predominant sequence variants of each isolate revealed almost similar grouping of isolates for each gene. The groups revealed by phylogenetic trees include sequences from isolates that cause severe quick decline, seedling yellows and stem pitting (SP) and also from mild isolates. The high percentage of mixed infections is alarming because of the threat of further diversification and spread of severe variants into additional citrus-growing areas of Pakistan and neighboring countries. Eleven CTV isolates from Pakistan were biologically indexed, and most induced mild or mild to moderate reactions on all biological indicators. Four genomic regions of isolate 21C from the biological indexing experiment were sequenced and phylogenetically analysed. These results provide the basis for mild strain cross protection (MSCP) in Pakistan and in neighbouring countries in the near future.

Keywords

Citrus tristeza virus isolates Genetic variability Phylogenetic cluster analysis Sour orange rootstock Biological indexing 

Notes

Acknowledgements

This study was supported by MOA’s Public Benefit Research Foundation of China (200903004-06), Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT, IRT0976) and MOA’s ‘948’ Project of China (2010-C23), Chinese Scholarship Council (CSC). Special thanks are extended to Prof. Li Zhong’an for his kind help. The experiments complied with the current laws of China and Pakistan.

Supplementary material

10327_2017_737_MOESM1_ESM.pdf (4.8 mb)
Supplementary material 1 (PDF 4939 KB)

References

  1. Al-Sadi A, Al-Hilali S, Al-Yahyai R, Al-Said F, Deadman M, Al-Mahmooli I, Nolasco G (2012) Molecular characterization and potential sources of Citrus tristeza virus in Oman. Plant Pathol 61:632–640CrossRefGoogle Scholar
  2. Atta S, Liu Y, Cao M, Yang F-Y, Zhou Y, Zhou C (2011) Molecular characterization of Citrus tristeza virus isolates from Pakistan based on CPG/Hinf I restriction fragment length polymorphism (RFLP) groups analysis. Afr J Biotech 10:8689–8694CrossRefGoogle Scholar
  3. Atta S, Zhou C-y, Yan Z, Cao M-j, Wang X-f (2012) Distribution and research advances of Citrus tristeza virus. J Integr Agric 11:346–358CrossRefGoogle Scholar
  4. Ayllón MaA, Gowda S, Satyanarayana T, Dawson WO (2004) cis-acting elements at opposite ends of the Citrus tristeza virus genome differ in initiation and termination of subgenomic RNAs. Virology 322:41–50CrossRefPubMedGoogle Scholar
  5. Baker KF (1957) The UC system for producing healthy container-grown plants through the use of clean soil, clean stock, and sanitation. University of California, Agricultural Experiment Station, Manual 23Google Scholar
  6. Bar-Joseph M, Marcus R, Lee RF (1989) The continuous challenge of citrus tristeza virus control. Annu Rev Phytopathol 27:291–316CrossRefGoogle Scholar
  7. Broadbent P, Brlansky R, Indsto J (1996) Biological characterization of Australian isolates of citrus tristeza virus and separation of subisolates by single aphid transmissions. Plant Dis 80:329–333CrossRefGoogle Scholar
  8. Catara A, Azzaro A, Mughal S, Khan D (1988) Virus, viroid and prokaryotic diseases of citrus in Pakistan. In: Goren R, Mendel K (eds), Citriculture, Proceedings of 6th International Citrus Conference, Middle-East, Tel Aviv, 6–11 March 1988, vol. 2 Cultural practices, diseases and nematodes. Balaban Publishers, Rehovot, pp 957–962Google Scholar
  9. Cevik B, Pappu S, Pappu H, Tight D, Benscher D, Futch S, Rucks P, Lee R, Niblett C (1996) Molecular cloning and sequencing of coat protein genes of citrus tristeza virus isolated from Meyer lemon and Homely Tangor trees in Florida. In: Proc 13th Conf Intern Organ Citrus Virol, Riverside, pp 47–53Google Scholar
  10. Davino S, Willemsen A, Panno S, Davino M, Catara A, Elena SF, Rubio L (2013) Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy. PloS One 8:e66700CrossRefPubMedPubMedCentralGoogle Scholar
  11. Domingo E, Holland JJ (1994) Mutation rates and rapid evolution of RNA viruses. The evolutionary biology of viruses. In: Morse SS (ed) Evolutionary biology of viruses. Raven Press, New York, pp 161–184Google Scholar
  12. Fagoaga C, López C, Moreno P, Navarro L, Flores R, Peña L (2005) Viral-like symptoms induced by the ectopic expression of the p23 gene of Citrus tristeza virus are citrus specific and do not correlate with the pathogenicity of the virus strain. Mol Plant Microbe Interact 18:435–445CrossRefPubMedGoogle Scholar
  13. Febres V, Ashoulin L, Mawassi M, Frank A, Bar-Joseph M, Manjunath K, Lee R, Niblett C (1996) The p27 protein is present at one end of citrus tristeza virus particles. Phytopathology 86:1331–1335Google Scholar
  14. Flores R, Ruiz-Ruiz S, Soler N, Sánchez-Navarro J, Fagoaga C, López C, Navarro L, Moreno P, Peña L (2013) Citrus tristeza virus p23: a unique protein mediating key virus–host interactions. Front Microbiol 4:98PubMedPubMedCentralGoogle Scholar
  15. Garnsey S, Gumpf D, Roistacher C, Civerolo E, Lee R, Yokomi R, Bar-Joseph M (1987) Toward a standardized evaluation of the biological properties of Citrus tristeza virus. Phytophylactica 19:151–157Google Scholar
  16. Garnsey SM, Permar TA, Cambra M, Henderson CT (1993) Direct tissue blot immunoassay (DTBIA) for detection of citrus tristeza virus (CTV). In: Proceedings of 12th conference of IOCV (India 1998), pp 39–50Google Scholar
  17. Ghorbel R, López C, Fagoaga C, Moreno P, Navarro L, Flores R, Peña L (2001) Transgenic citrus plants expressing the citrus tristeza virus p23 protein exhibit viral-like symptoms. Mol Plant Pathol 2:27–36CrossRefPubMedGoogle Scholar
  18. Gowda S, Satyanarayana T, Davis CL, Navas-Castillo J, Albiach-Martí MR, Mawassi M, Valkov N, Bar-Joseph M, Moreno P, Dawson WO (2000) The p20 gene product of Citrus tristeza virus accumulates in the amorphous inclusion bodies. Virology 274:246–254CrossRefPubMedGoogle Scholar
  19. Harper SJ (2013) Citrus tristeza virus: evolution of complex and varied genotypic groups. Front Microbiol 4:93CrossRefPubMedPubMedCentralGoogle Scholar
  20. Hilf ME, Karasev AV, Pappu HR, Gumpf DJ, Niblett CL, Garnsey SM (1995) Characterization of citrus tristeza virus subgenomic RNAs in infected tissue. Virology 208:576–582CrossRefPubMedGoogle Scholar
  21. Iftikhar Y, Khan MA, Rashid A, Mughal S, Iqbal Z, Batool A, Abbas M, Khan M, Muhammad S, Jaskani M (2009) Occurrence and distribution of citrus tristeza closterovirus in the Punjab and NWFP, Pakistan. Pak J Bot 41:373–380Google Scholar
  22. Iglesias NG, Gago-Zachert SP, Robledo G, Costa N, Plata MI, Vera O, Grau O, Semorile LC (2008) Population structure of Citrus tristeza virus from field Argentinean isolates. Virus Genes 36:199–207CrossRefPubMedGoogle Scholar
  23. Jiang B, Hong N, Wang G-P, Hu J, Zhang J-K, Wang C-X, Liu Y, Fan X-D (2008) Characterization of Citrus tristeza virus strains from southern China based on analysis of restriction patterns and sequences of their coat protein genes. Virus Genes 37:185–192CrossRefPubMedGoogle Scholar
  24. Karasev A, Boyko V, Gowda S, Nikolaeva O, Hilf M, Koonin E, Niblett C, Cline K, Gumpf D, Lee R (1995) Complete sequence of the citrus tristeza virus RNA genome. Virology 208:511–520CrossRefPubMedGoogle Scholar
  25. Kong P, Rubio L, Polek M, Falk BW (2000) Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates. Virus Genes 21:139–145CrossRefPubMedGoogle Scholar
  26. Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306CrossRefPubMedPubMedCentralGoogle Scholar
  27. Long Y, Zhou C-Y, Yan Z, Li Z-A (2010) Genetic evolution analysis on wild isolates of Citrus tristeza virus originated in China based on coat protein genes sequences. Agric Sci China 9:1623–1629CrossRefGoogle Scholar
  28. López C, Navas-Castillo J, Gowda S, Moreno P, Flores R (2000) The 23-kDa protein coded by the 3′-terminal gene of citrus tristeza virus is an RNA-binding protein. Virology 269:462–470CrossRefPubMedGoogle Scholar
  29. Lu R, Folimonov A, Shintaku M, Li W-X, Falk BW, Dawson WO, Ding S-W (2004) Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Nat Acad Sci USA 101:15742–15747CrossRefPubMedPubMedCentralGoogle Scholar
  30. Moreno P, AmbrOS S, Albiach-Martí MR, Guerri J, Peña L (2008) Citrus tristeza virus: a pathogen that changed the course of the citrus industry. Mol Plant Pathol 9:251–268CrossRefPubMedGoogle Scholar
  31. Pappu H, Karasev A, Anderson E, Pappu S, Hilf M, Febres V, Eckloff R, McCaffery M, Boyko V, Gowda S (1994) Nucleotide sequence and organization of eight 3′ open reading frames of the citrus tristeza closterovirus genome. Virology 199:35–46CrossRefPubMedGoogle Scholar
  32. Rubio L, Ayllón MA, Kong P, Fernández A, Polek M, Guerri J, Moreno P, Falk BW (2001) Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol 75:8054–8062CrossRefPubMedPubMedCentralGoogle Scholar
  33. Ruiz-Ruiz S, Soler N, Sánchez-Navarro J, Fagoaga C, López C, Navarro L, Moreno P, Peña L, Flores R (2013) Citrus tristeza virus p23: determinants for nucleolar localization and their influence on suppression of RNA silencing and pathogenesis. Mol Plant Microbe Interact 26:306–318CrossRefPubMedGoogle Scholar
  34. Sambade A, López C, Rubio L, Flores R, Guerri J, Moreno P (2003) Polymorphism of a specific region in gene p23 of Citrus tristeza virus allows discrimination between mild and severe isolates. Arch Virol 148:2325–2340CrossRefPubMedGoogle Scholar
  35. Satyanarayana T, Gowda S, Mawassi M, Albiach-Martí R, Ayllón A, Robertson C, Garnsey SM, Dawson WO (2000) Closterovirus encoded HSP70 homolog and p61 in addition to both coat proteins function in efficient virion assembly. Virology 278:253–265CrossRefPubMedGoogle Scholar
  36. Satyanarayana T, Gowda S, Ayllón MA, Dawson WO (2004) Closterovirus bipolar virion: evidence for initiation of assembly by minor coat protein and its restriction to the genomic RNA 5′ region. Proc Nat Acad Sci USA 101:799–804CrossRefPubMedPubMedCentralGoogle Scholar
  37. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedPubMedCentralGoogle Scholar
  38. Zhou C, Hailstones D, Connor R, Barkley P, Bowyer J (2001) A micro and rapid nucleotide acid extraction method of Citrus tristeza virus for amplification by RT-PCR. J Fujian Agric For Univ 30:200Google Scholar

Copyright information

© The Phytopathological Society of Japan and Springer Japan KK 2017

Authors and Affiliations

  • Sagheer Atta
    • 1
    • 2
  • Mengji Cao
    • 1
    • 3
  • Ummad ud din Umar
    • 4
  • Yan Zhou
    • 1
  • Fangyun Yang
    • 1
  • Changyong Zhou
    • 1
    Email author
  1. 1.National Citrus Engineering Research Center, Citrus Research InstituteSouthwest UniversityChongqingChina
  2. 2.Faculty of Agricultural SciencesGhazi UniversityDera Ghazi KhanPakistan
  3. 3.College of Plant ProtectionSouthwest UniversityChongqingChina
  4. 4.Department of Plant PathologyBahauddin Zakariya UniversityMultanPakistan

Personalised recommendations