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Molecular characterization and sequence analyses of Banana bunchy top virus infecting banana cultivar Jahaji (Dwarf Cavendish) in Assam, India

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Abstract

Several isolates of Banana bunchy top virus (BBTV) have been reported worldwide. They are members of either the Pacific Indian Ocean (PIO) or the South East Asian (SEA) group. However, there is only one completely sequenced isolate published from the northeastern part of India till date. Therefore, we obtained the complete sequences of all the six genomic components of a BBTV isolate from the northeastern Indian state of Assam. The isolate was named as BBTV-As-JOR, and its genome showed the presence of the reported conserved motifs. Nevertheless, like other Indian BBTV isolate, the major common regions in DNA-R and DNA-U3 of BBTV-As-JOR had deletions of 26 and 36 nucleotides, respectively. Phylogenetic analysis based on 312 sequences of BBTV DNA-R classified BBTV-As-JOR as a member of the PIO group; similar phylogenetic patterns were also found with the other genomic segments. Analysis with Recombination Detection Program revealed two intra-segment recombination events involving DNA-C of geographically distinct BBTV isolates. On the other hand, DNA-U3 and DNA-N were found to be involved in few inter-segment recombination events in BBTV-As-JOR. This is the first report of a BBTV isolate from Assam and also of another PIO isolate from the region (the other isolate, BBTV-Umiam, was much closer to the SEA group). The detected possible recombinants could emerge as a major future threat for the banana cultivations in the country considering the asexual nature of propagation of banana crop.

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Acknowledgements

This work was funded by Department of Science and Technology, Govt of India (GoI; grant number: SERB/F/5181/2012-13). Research in the Department of Agricultural Biotechnology (ABT), Assam Agricultural University (AAU) is also funded by Department of Biotechnology (DBT), GoI; Indian Council of Agricultural Research, GoI and DBT-AAU Centre. The authors thank the Distributed Information Centre, ABT, for providing computational facility. GMB acknowledges University Grants Commission, GoI for providing Rajiv Gandhi National fellowship (RGNF-2015-17-SC-RAJ-6919). The authors thank Dr K.M. Bujarbaruah, Vice Chancellor and Dr B.K. Sarmah, DBT-AAU Centre for their suggestions at various stages.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India

    Gajendra Mohan Baldodiya, Geetanjali Baruah, Basanta Kumar Borah & Mahendra Kumar Modi

  2. Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam, 785013, India

    Palash Deb Nath

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  1. Gajendra Mohan Baldodiya
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  2. Geetanjali Baruah
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  3. Basanta Kumar Borah
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  4. Mahendra Kumar Modi
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  5. Palash Deb Nath
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Contributions

BKB and GMB conceptualized and designed the study; GMB, with the help of GB, performed the sample collection, wet lab experiments and in silico analysis. PDN and MKM helped BKB to design the study. GMB prepared and BKB finalized the manuscript. All the authors reviewed the manuscript.

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Correspondence to Basanta Kumar Borah.

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Research involving animal and human participants

This article does not contain any studies with human participants or animals performed by any of the authors.

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ESM_1 Details of primers used for amplification of the six DNA segments of BBTV [22]

ESM_2 Details of the walking primers used for full-length sequencing of DNA-R, DNA-S, DNA-M, DNA-C and DNA-N

ESM_3 BBTV isolates used for inter-segment recombination analysis

ESM_4 The stem loop regions in the DNA-R, DNA-U3, DNA-S, DNA-M, DNA-C and DNA-N of BBTV-As-JOR. The hair-pin structures of each segment are represented in bold fonts

ESM_5 Phylogenetic analysis of the (a) DNA-U3, (b) DNA-S, (c) DNA-M, (d) DNA-C and (e) DNA-N based on nucleotide sequence similarity. Two ABTV isolates were included to make a separate an out-group. BBTV-As-JOR is shown in bold texts

ESM_6 Intra-segment recombination analysis of the six genomic components of the BBTV segments available in database. The sequences of BBTV-As-JOR are in bold fonts. The sequences were retrieved on 18-8-2017 at 9.14 AM

ESM_7 Inter-segment recombination analysis of the six genomic components 121 BBTV isolates available with full-length sequences in the database. The sequences of BBTV-As-JOR are in bold fonts. The sequences were retrieved on 20-8-2017 at 10.17 AM

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Baldodiya, G.M., Baruah, G., Borah, B.K. et al. Molecular characterization and sequence analyses of Banana bunchy top virus infecting banana cultivar Jahaji (Dwarf Cavendish) in Assam, India. 3 Biotech 9, 110 (2019). https://doi.org/10.1007/s13205-019-1636-5

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