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Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India

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Abstract

Rice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2–68 nucleotides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differences were not significant as revealed by Ka/Ks ratio calculation. Sequence identity at nucleotide and amino acid level was 92–100% and 97–100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus.

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Acknowledgments

Authors are highly thankful to Dr. R.M. Sundaram (Senior Scientist, Directorate of Rice Research, Hyderabad) for providing the tungro infected rice samples of Puducherry. Financial support obtained under the SERC fast track scheme of Department of Science and Technology (DST), Govt. of India is highly acknowledged.

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Authors and Affiliations

  1. Biotechnology Section, Directorate of Rice Research, Hyderabad, Andhra Pradesh, 500030, India

    Satendra K. Mangrauthia, P. Malathi, Surekha Agarwal, G. Ramkumar, C. N. Neeraja, M. Sheshu Madhav & S. M. Balachandran

  2. Division of Plant Pathology, Directorate of Rice Research, Hyderabad, Andhra Pradesh, 500030, India

    D. Krishnaveni & D. Ladhalakshmi

  3. Directorate of Rice Research, Hyderabad, Andhra Pradesh, 500030, India

    B. C. Viraktamath

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  1. Satendra K. Mangrauthia
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  2. P. Malathi
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  3. Surekha Agarwal
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  4. G. Ramkumar
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  5. D. Krishnaveni
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  6. C. N. Neeraja
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  7. M. Sheshu Madhav
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  8. D. Ladhalakshmi
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  9. S. M. Balachandran
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  10. B. C. Viraktamath
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Correspondence to Satendra K. Mangrauthia.

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Mangrauthia, S.K., Malathi, P., Agarwal, S. et al. Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India. Virus Genes 44, 482–487 (2012). https://doi.org/10.1007/s11262-011-0708-3

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  • DOI: https://doi.org/10.1007/s11262-011-0708-3

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