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First report of the complete genomic sequences from Indonesian isolates of bamboo mosaic virus and detection of genomic recombination events

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Abstract

Bamboo mosaic virus belongs to the genus Potexvirus, family Alphaflexiviridae. Bamboo leaves with chlorotic mosaic were collected from Yogyakarta, Indonesia, and RT-PCR and sequence analyses determined that the causal agent was bamboo mosaic virus (BaMV). The genome, excluding the poly(A) tail, of Indonesian isolate BaMV-Yogya1 comprised 6364 nucleotides and 6365 nucleotides for BaMV-Yogya2. Both isolates had higher similarities to Taiwanese isolates than to Chinese isolates. A recombination detection program suggested that recombination occurred within the ORF1 and ORF5 regions of BaMV-Yogya1. This is the first report of the complete genome sequence of BaMV from Indonesia.

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Acknowledgements

T. N. received a Grant-in-Aid for Scientific Research, category B (JSPS KAKENHI, grant nos. 26304023 and 17H04617). We thank Lesley Benyon, Ph.D., from Edanz Group (http://www.edanzediting.com/ac) for editing a draft of this manuscript.

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Authors and Affiliations

  1. School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan

    Satomi Abe, Yutaro Neriya, Kengo Noguchi, Hisashi Nishigawa & Tomohide Natsuaki

  2. Department of Crop Protection, Faculty of Agriculture, Gadjah Mada University, Jl. Flora 1, Bulaksumur, Yogyakarta, 55281, Indonesia

    Sedyo Hartono, Sri Sulandari & Susamto Somowiyarjo

  3. Department of Plant Pathology, The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, 25130, Pakistan

    Asad Ali

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  1. Satomi Abe
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  2. Yutaro Neriya
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  4. Sedyo Hartono
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Corresponding author

Correspondence to Yutaro Neriya.

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

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The authors declare that they have no conflict of interest.

Additional information

The GenBank/ENA/DDBJ accession no. of the sequences of BaMV-Yogya1 and BaMV-Yogya2: LC278458 and LC278459.

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10327_2018_830_MOESM1_ESM.docx

Fig. S1 (a) Analysis of recombination among BaMV isolates. The genome sequence of BaMV-Yogya1 compared with that of the BaMV isolates (BaMV-Yogya2, green; BaMV-Au, red; BaMV-Bo, blue; BaMV-Pu, light blue; BaMV-O, gray) in a SimPlot analysis. The results of the SimPlot analysis were exported with a 200-nt window in 20-nt steps. The genome structure of BaMV is at the top. The neighbor-joining phylogenetic tree of available BaMV isolate sequences based on (b) nt 743–3557, (c) nt 5542–6066 and (d) combined sequences of nt 1–742, 3558–5541 and 6067–6364 (positions refer to BaMV-Yogya1). BaMV Chinese isolates were used as the outgroup. Numbers on branches are bootstrap values (%) obtained from 1,000 replicates; only values > 60% are shown. Phylogenetic trees with maximum likelihood or maximum parsimony method had the same topology as the neighbor-joining tree. Scale bars indicate number of base substitutions per site. GenBank/ENA/DDBJ accession nos.; BaMV-Au (AB636267), BaMV-Bo (AB543679), BaMV-Pu (AB636266), BaMV-V (L77962), BaMV-O (D26017) and BaMV-S (AF018156) (DOCX 137 KB)

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Abe, S., Neriya, Y., Noguchi, K. et al. First report of the complete genomic sequences from Indonesian isolates of bamboo mosaic virus and detection of genomic recombination events. J Gen Plant Pathol 85, 158–161 (2019). https://doi.org/10.1007/s10327-018-0830-3

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  • DOI: https://doi.org/10.1007/s10327-018-0830-3

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