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Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein

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Abstract

The complete sequences of the coat protein (CP) gene of 26 isolates of Apple chlorotic leaf spot virus (ACLSV) from India were determined. The isolates were obtained from various pome (apple, pear and quince) and stone (plum, peach, apricot, almond and wild Himalayan cherry) fruit trees. Other previously characterized ACLSV isolates and Trichoviruses were used for comparative analysis. Indian ACLSV isolates among themselves and with isolates from elsewhere in the world shared 91–100% and 70–98% sequence identities at the amino acid and nucleotide levels, respectively. The highest degree of variability was observed in the middle portion with 9 amino acid substitutions in contrast to the N-terminal and C-terminal ends, which were maximally conserved with only 4 amino acid substitutions. In phylogenetic analysis no reasonable correlation between host species and/or geographic origin of the isolates was observed. Alignment with capsid protein genes of other Trichoviruses revealed the TaTao ACLSV peach isolate to be phylogenetically closest to Peach mosaic virus, Apricot pseudo chlorotic leaf spot virus and Cherry mottle leaf virus. Recombination analysis (RDP3 ver.2.6) done for all the available ACLSV complete CP sequences of the world and Indian isolates indicate no significant evidence of recombination. However, one recombination event among Indian ACLSV-CP isolates was detected. To the best of our knowledge, this is the first report of complete CP sequence variability study from India and also the first evidence of homologous recombination in ACLSV.

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Abbreviations

ACLSV:

Apple chlorotic leaf spot virus

CP coat protein:

DAS, double antibody sandwich

PREs:

potential recombination events

RDP:

Recombination Detection Program

RT-PCR:

reverse transcription-polymerase chain reaction

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Authors and Affiliations

  1. Plant Virology Lab, Institute of Himalayan Bioresource Technology, Palampur, 176 061, India

    T. Rana, V. Chandel, Y. Kumar, R. Ram, V. Hallan & A. A. Zaidi

Authors
  1. T. Rana
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  2. V. Chandel
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  3. Y. Kumar
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  4. R. Ram
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  5. V. Hallan
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  6. A. A. Zaidi
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Correspondence to A. A. Zaidi.

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Supplementary figures pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/Dec2010/pp605-615/suppl.pdf

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Rana, T., Chandel, V., Kumar, Y. et al. Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein. J Biosci 35, 605–615 (2010). https://doi.org/10.1007/s12038-010-0069-4

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  • DOI: https://doi.org/10.1007/s12038-010-0069-4

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