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The molecular diversity and evolution of Rice tungro bacilliform virus from Indian perspective

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Abstract

Rice tungro disease is caused by a combination of two viruses: Rice tungro spherical virus and Rice tungro bacilliform virus (RTBV). This study was performed with the objective to decipher the molecular variability and evolution of RTBV isolates present in the tungro-affected states of Indian subcontinent. Phylogenetic analysis based on ORF-I, ORF-II, and ORF-IV sequences showed distinct divergence of Indian RTBV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Chinsura West Bengal, and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic analysis were further supported with the single nucleotide polymorphisms (SNPs), insertion and deletion (INDELs) and evolutionary distance analysis. In addition, sequence difference count matrix revealed a maximum of 56 (ORF-I), 13 (ORF-II) and 73 (ORF-IV) nucleotides differences among all the Indian RTBV isolates taken in this study. However, at the protein level these differences were not significant as revealed by K a/K s ratio calculation. Sequence identity at nucleotide and amino acid level was 92–100 % (ORF-I), 96–100 % (ORF-II), 94–100 % (ORF-IV) and 86–100 % (ORF-I), 98–100 % (ORF-II) and 95–100 % (ORF-IV), respectively, among Indian isolates of RTBV. The divergence of RTBV isolates into two independent clusters of Indian and non-Indian was shown with the help of the data obtained from phylogeny, SNPs, and INDELs, evolutionary distance analysis, and conserved motifs analysis. The important role of ORF-I and ORF-IV in RTBV diversification and adaptation to different rice growing regions is also discussed.

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Acknowledgments

Authors are highly thankful to the Project Director, DRR for constant support and encouragement. The financial support obtained from Fast track scheme of Department of Science and Technology, Govt. of India is highly acknowledged. B. Sailaja acknowledges the fellowship and financial support obtained from National Initiative on Climate Resilient Agriculture (NICRA) Project.

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Authors and Affiliations

  1. Directorate of Rice Research, Hyderabad, India

    Satendra K. Mangrauthia, P. Malathi, Surekha Agarwal, B. Sailaja, G. Ramkumar, D. Krishnaveni & S. M. Balachandran

  2. Bundelkhand University, Jhansi, India

    Jagrati Singh

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  1. Satendra K. Mangrauthia
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  2. P. Malathi
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Correspondence to Satendra K. Mangrauthia.

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Mangrauthia, S.K., Malathi, P., Agarwal, S. et al. The molecular diversity and evolution of Rice tungro bacilliform virus from Indian perspective. Virus Genes 45, 126–138 (2012). https://doi.org/10.1007/s11262-012-0751-8

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  • DOI: https://doi.org/10.1007/s11262-012-0751-8

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