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Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus

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Abstract

Banana bunchy top virus (BBTV) is a multi-component single-stranded DNA virus. From 267 potentially infected Musa plants, 24 apparently ‘defective’ BBTV components have been identified. Interestingly, 23/24 of these defective molecules were apparently derived from DNA-R. All of the identified defective molecules had retained at least part of the CR-SL and CR-M but had insertions and/or deletions that in most cases resulted in open reading frame disruptions. Our detection of three monophyletic but diverse (and therefore likely circulating) defective DNA-R lineages suggests that, in many cases, defective DNA-R molecules might remain associated with BBTV genomes for prolonged periods.

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Acknowledgments

D.S was supported by a postgraduate scholarship from the Marsden Fund of New Zealand (UOC0903). AV and DPM are supported by the National Research Foundation of South Africa. This work was supported by the Marsden Fund Council from government funding, administered by the Royal Society of New Zealand (grant UOC0903) awarded to AV.

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Authors and Affiliations

  1. School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand

    Daisy Stainton, David A. Collings & Arvind Varsani

  2. Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa

    Darren P. Martin & Arvind Varsani

  3. Ecosciences Precinct, Queensland Alliance for Agriculture and Food Innovation, Centre for Plant Science, The University of Queensland, PO Box 46, Brisbane, QLD, 4001, Australia

    John E. Thomas

  4. Department of Plant Pathology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA

    Arvind Varsani

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  1. Daisy Stainton
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Corresponding author

Correspondence to Arvind Varsani.

Electronic supplementary material

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Supplementary Data 1 Fasta file of defective BBTV sequences (TXT 25 kb)

705_2015_2736_MOESM2_ESM.pdf

Supplementary Figure 1 Insert and deletion breakpoint distribution plot where total numbers of breakpoints falling within a 200-nt moving window have been plotted across DNA-R (black line). Points where the black line emerges above the dark grey (95% confidence interval on the expected number of breakpoints at particular genome sites) and light grey (99% confidence interval) areas indicate statistically significant degrees of breakpoint clustering. Two breakpoint hotspots detected at a p–value significance threshold ≤ 0.01) are highlighted in red. (PDF 361 kb)

705_2015_2736_MOESM3_ESM.pdf

Supplementary Figure 2 Maximum-likelihood phylogenetic tree of the rep coding region of the defective DNA-R molecule sequences (insert regions removed) and 302 DNA-R components (see Supplementary Table 1). The phylogenetic tree was rooted with ABTV DNA-R sequences, and branches with < 60% bootstrap support were collapsed. Isolate information is available in Supplementary Table 1 for the DNA-R sequences and in Table 1 for the defective genomes (PDF 977 kb)

705_2015_2736_MOESM4_ESM.doc

Supplementary Table 1 List of DNA-R sequences used in Figure 2 with two-letter country codes: AU, Australia; BI, Burundi; CD, Democratic Republic of Congo; CG, Congo; CN, China; EG, Egypt; FJ, Fiji; ID, Indonesia; IN, India; JP, Japan; LK, Sri Lanka; MM, Myanmar; MY, Malaysia; MW, Malawi; PH, Philippines; PK, Pakistan; RW, Rwanda; TO, Tonga; TW, Taiwan; US, United States of America; VN, Vietnam; WS, Samoa (DOC 282 kb)

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Stainton, D., Martin, D.P., Collings, D.A. et al. Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus. Arch Virol 161, 1019–1026 (2016). https://doi.org/10.1007/s00705-015-2736-0

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