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Virology/Virologie

Genetic diversity and evolution of Apple stem pitting virus isolates from pear in China

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Pages 218-230 | Accepted 23 Feb 2016, Published online: 23 Mar 2016

References

  • Adams MJ, Lefkowitz EJ, King AM, Carstens EB. 2014. Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses (2014). Arch Virol. 159:2831–2841.
  • Aglayan K, Sere IU, Gazel M, Jelkmann W. 2006. Detection of four apple viruses by ELISA and RT-PCR assays in Turkey. Turk J Agric For. 4:241–246.
  • Alabi OJ, Martin RR, Naidu RA. 2010. Sequence diversity, population genetics and potential recombination events in Grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards. J Gen Virol. 91:265–276.
  • Bandín I, Dopazo CP. 2011. Host range, host specificity and hypothesized host shift events among viruses of lower vertebrates. Veter Res. 42:544.
  • Boni MF, Posada D, Feldman MW. 2007. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics. 176:1035–1047.
  • Boulila M. 2010. Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis. Biochem Genet. 48:357–375.
  • Dhir S, Tomar M, Thakur PD, Ram R, Hallan V, Zaidi AA. 2010. Molecular evidence for Apple stem pitting virus infection in India. Plant Pathol. 59:393.
  • Farooq AB, Ma YX, Wang ZQ, Zhuo N, Xu W, Wang GP, Hong N. 2013. Genetic diversity analyses reveal novel recombination events in Grapevine leafroll-associated virus 3 in China. Virus Res. 171:15–21.
  • Glasa M, Palkovics L, Komínek P, Labonne G, Pittnerová S, Kúdela O, Candresse T, Subr Z. 2004. Geographically and temporally distant natural recombinant isolates of Plum pox virus (PPV) are genetically very similar and form a unique PPV subgroup. J Gen Virol. 85:2671–2681.
  • Heath L, Van der Walt E, Varsani A, Martin DP. 2006. Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol. 80:11827–11832.
  • Holmes EC. 2010. The evolution and emergence of RNA viruses. New York: Oxford University Press.
  • James D, Varga A, Jesperson GD, Navratil M, Safarova D, Constable F, Horner M, Eastwell K, Jelkmann W. 2013. Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease. Arch Virol. 158:1877–1887.
  • Jelkmann W. 1994. Nucleotide sequences of Apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses. J Gen Virol. 75:1535–1542.
  • Jelkmann W, Keim-Konrad R. 1997. Immuno-capture polymerase chain reaction and plate-trapped ELISA for the detection of Apple stem pitting virus. J Phytopathol. 145:499–503.
  • Klerks MM, Leone G, Lindner JL, Schoen CD, Van den Heuvel JF. 2001. Rapid and sensitive detection of Apple stem pitting virus in apple trees through RNA amplification and probing with fluorescent molecular beacons. Phytopathology. 91:1085–1091.
  • Komorowska B, Malinowski T, Michalczuk L. 2010. Evaluation of several RT-PCR primer pairs for the detection of Apple stem pitting virus. J Virol Meth. 168:242–247.
  • Komorowska B, Siedlecki P, Kaczanowski S, Hasiów-Jaroszewska B, Malinowski T. 2011. Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus. Virus Res. 158:263–267.
  • Kundu JK. 2003. The occurrence of Apple stem pitting virus and Apple stem grooving virus within field-grown apple cultivars evaluated by RT-PCR. Plant Prot Sci. 88–92.
  • Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G. 2008. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. J Virol Meth. 154:48–55.
  • Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Liu N, Niu J, Zhao Y. 2012. Complete genomic sequence analyses of Apple stem pitting virus isolates from China. Virus Genes. 44:124–130.
  • Martelli GP, Jelkmann W. 1998. Foveavirus, a new plant virus genus. Arch Virol. 143:1245–1249.
  • Martin DP, Posada D, Crandall KA, Williamson C. 2005. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. Aids Res Human Retrov. 21:98–102.
  • Martín S, Sambade A, Rubio L, Vives MC, Moya P, Guerri J, Elena SF, Moreno P. 2009. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J Gen Virol. 90:1527–1538.
  • Mathioudakis MM, Katis NI. 2006. First record of the Apple stem pitting virus (ASPV) in quince in Greece. J Plant Pathol. 88:221.
  • Mathioudakis MM, Maliogka VI, Dovas CI, Paunović S, Katis NI. 2009. Reliable RT-PCR detection of Apple stem pitting virus in pome fruits and its association with quince fruit deformation disease. Plant Pathol. 58:228–236.
  • Mathioudakis MM, Maliogka VI, Katsiani AT, Katis NI. 2010. Incidence and molecular variability of Apple stem pitting and Apple chlorotic leaf spot viruses in apple and pear orchards in Greece. J Plant Pathol. 92:139–147.
  • Menzel W, Jelkmann W, Maiss E. 2002. Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. J Virol Meth. 99:81–92.
  • Moya A, Holmes EC, González-Candelas F. 2004. The population genetics and evolutionary epidemiology of RNA viruses. Nat Rev Microbiol. 2:279–288.
  • Padidam M, Sawyer S, Fauquet CM. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology. 265:218–225.
  • Posada D, Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci USA. 98:13757–13762.
  • Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. 2004. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496–2497.
  • Senshu H, Ozeki J, Komatsu K, Hashimoto M, Hatada K, Aoyama M, Kagiwada S, Yamaji Y, Namba S. 2009. Variability in the level of RNA silencing suppression caused by triple gene block protein 1 (TGBp1) from various potexviruses during infection. J Gen Virol. 90:1014–1024.
  • Seo JK, Ohshima K, Lee HG, Son M, Choi HS. 2009. Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences. Virology. 393:91–103.
  • Smith JM. 1992. Analyzing the mosaic structure of genes. J Mol Evol. 34:126–129.
  • Solovyev AG, Kalinina NO, Morozov SY. 2012. Recent advances in research of plant virus movement mediated by triple gene block. Front Plant Sci. 3:276.
  • Syrgianidis GD. 1989. Problems of virus diseases of deciduous fruit trees in Greece. Acta Horticul. 21–26.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882.
  • Valli A, López-Moya JJ, García JA. 2007. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol. 88:1016–1028.
  • Verchot-Lubicz J, Torrance L, Solovyev AG, Morozov SY, Jackson AO, Gilmer D. 2010. Varied movement strategies employed by triple gene block-encoding viruses. Mol Plant-Microbe Inter. 23:1231–1247.
  • Voinnet O, Cederer C, Baulcombe DC. 2000. A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell. 103:157–167.
  • Wang PG, Hong N, Zhong PZ, Hu CS, Dong ZY. 1994. Identification of kinds of viruses for main pear cultivars in pear growing areas in northern China. China Fruits. 5:1–4.
  • Wu ZB, Ku HM, Su CC, Chen IZ, Jan FJ. 2010. Molecular and biological characterization of an isolate of Apple stem pitting virus causing pear vein yellows disease in Taiwan. J Plant Pathol. 92:721–728.
  • Yoon JY, Joa JH, Choi KS, Do KS, Lim HC, Chung BN. 2014. Genetic diversity of a natural population of Apple stem pitting virus isolated from apple in Korea. Plant Pathol J. 30:195–199.
  • Youssef SA, Moawad SM, Nosseir FM, Shalaby AA. 2010. Detection and identification of Apple stem pitting virus and Apple stem grooving virus affecting apple and pear trees in Egypt. Julius-Kühn-Archiv. 427:248.
  • Zhang CL, Gao R, Wang J, Zhang GM, Li XD, Liu HT. 2011. Molecular variability of Tobacco vein banding mosaic virus populations. Virus Res, 158:188–198.

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