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Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution

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Abstract

A new isolate of Rice tungro bacilliform virus (RTBV) was collected from Chinsura, West Bengal, India. The full genome was sequenced and deposited to GenBank designating the new one as Chinsura isolate. The four open reading frames (ORFs) of the new isolate were compared with those of previously reported ‘South-east Asian’ (SEA) and ‘South Asian’ (SA) isolates emphasizing the ORF3, which is the largest and functionally most important gene of RTBV. In the ORFs, Chinsura isolate shared 90.0–100.0% identity at amino acid level with SA isolates, but only 58.76–88.63% identity with SEA isolates for the same. Similarly, the amino acid identity of ORFs between SEA and SA isolates ranged from 58.77 to 88.64, whereas within each group the corresponding value was >96.0%. The phylogenetic analysis based on nucleotide and amino acid sequences of each ORF made two broad clusters of SEA- and SA-types including Chinsura isolate within SA cluster. Moreover, the relative positions and length of functional domains corresponding to movement protein (MP), coat protein (CP), aspartate protease (PR) and reverse transcriptase/ribonuclease H (RT/RNase H) of ORF3 of Chinsura isolate were completely identical with SA isolates. The clustering pattern indicated strong influence of geographical habitat on genomic evolution. Comparison of ORF3 among all the isolates revealed major variations at non-functional regions in between the functional domains and at the hypervariable 3′-terminal end of ORF3, while PR appeared to have evolved differentially in SA isolates expecting further characterization.

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Acknowledgments

The authors wish to thank Dr. Pinaki Bandopadhyay, Plant Pathologist, Rice Research Station, Government of West Bengal, Chinsura, for providing the tungro-infected leaf samples and other necessary supports.

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Author notes

  1. Amrita Banerjee

    Present address: Division of Plant Pathology, ICAR Research Complex for NEH Region, Umiam, Meghalya, 793103, India

  2. Somnath Roy

    Present address: NBPGR Regional Station-Shillong, Umiam, Meghalaya, 793103, India

Authors and Affiliations

  1. Department of Plant Pathology, BCKV, Mohanpur, Nadia, West Bengal, 741252, India

    Amrita Banerjee & Jayanta Tarafdar

  2. Department of Plant Breeding, BCKV, Mohanpur, Nadia, West Bengal, 741252, India

    Somnath Roy

Authors
  1. Amrita Banerjee
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  2. Somnath Roy
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  3. Jayanta Tarafdar
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Corresponding author

Correspondence to Amrita Banerjee.

Additional information

Amrita Banerjee and Somnath Roy contributed equally to this study.

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Banerjee, A., Roy, S. & Tarafdar, J. Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution. Virus Genes 43, 398–408 (2011). https://doi.org/10.1007/s11262-011-0647-z

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  • DOI: https://doi.org/10.1007/s11262-011-0647-z

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