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The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates

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Abstract

In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95 % to east Indian isolates and 90 % to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5′ end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

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Acknowledgments

Financial support received from NICRA (National Initiative on Climate and Resilient Agriculture) project is acknowledged.

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Authors and Affiliations

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

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

  2. Centre for Biotechnology, Institute of Science & Technology, Jawaharlal Nehru Technological University, Hyderabad, India

    Najreen Anjum

  3. Department of Biotechnology, Majhighariani Institute of Technology & Science, Biju Patnaik University of Technology, Rourkela, India

    Yogesh K. Patil

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  1. B. Sailaja
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  2. Najreen Anjum
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  5. P. Malathi
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  8. B. C. Viraktamath
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Correspondence to Satendra K. Mangrauthia.

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Sailaja, B., Anjum, N., Patil, Y.K. et al. The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates. Virus Genes 47, 515–523 (2013). https://doi.org/10.1007/s11262-013-0964-5

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