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Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus

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Abstract

Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72–97% nt sequence identity; 83–99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.

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Acknowledgments

The authors are grateful to Dr. N. Vijayan Nair, Director of the Institute, for encouragement and providing necessary facilities to carry out the work.

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Authors and Affiliations

  1. Plant Pathology Section, Division of Crop Protection, Sugarcane Breeding Institute, ICAR, Coimbatore, 641007, India

    K. Bagyalakshmi, C. Chinnaraja, R. Karuppaiah, V. Ganesh Kumar & R. Viswanathan

  2. Sugarcane Breeding Institute Regional Centre, Karnal, 132001, Haryana, India

    B. Parameswari

Authors
  1. K. Bagyalakshmi
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  2. B. Parameswari
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  3. C. Chinnaraja
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  4. R. Karuppaiah
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  5. V. Ganesh Kumar
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  6. R. Viswanathan
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Corresponding author

Correspondence to R. Viswanathan.

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Bagyalakshmi, K., Parameswari, B., Chinnaraja, C. et al. Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus. Arch Virol 157, 1371–1375 (2012). https://doi.org/10.1007/s00705-012-1297-8

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  • DOI: https://doi.org/10.1007/s00705-012-1297-8

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