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Genome organisation and sequence comparison suggest intraspecies incongruence in M RNA of Watermelon bud necrosis virus

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Abstract

Watermelon bud necrosis virus (WBNV), a member of the genus Tospovirus, family Bunyaviridae is an important viral pathogen in watermelon cultivation in India. The complete genome sequence properties of WBNV are not available. In the present study, the complete M RNA sequence and the genome organisation of a WBNV isolate infecting watermelon in Delhi (WBNV-wDel) were determined. The M RNA was 4,794 nucleotides (nt) long and potentially coded for a movement protein (NSm) of 34.22 kDa (307 amino acids) on the viral sense strand and a Gn/Gc glycoprotein precursor of 127.15 kDa (1,121 amino acids) on the complementary strand. The two open reading frames were separated by an intergenic region of 402 nt. The 5′ and 3′ untranslated regions were 55 and 47 nt long, respectively, containing complementary termini typical of tospoviruses. WBNV-wDel was most closely related (79.1% identity) to Groundnut bud necrosis virus, an important tospovirus that occurs in several crops in India, and was different (63.3–75.2% identity) from the other cucurbit-infecting tospoviruses known to occur in Taiwan and Japan. Sequence analysis of NSm and Gn/Gc revealed phylogenetic incongruence between WBNV-wDel and another isolate originating from central India (WBNV-Wm-Som isolate). The Wm-Som isolate showed evolutionary divergence from the wDel isolate in the Gn/Gc protein (74.6% identity) potentially due to recombination with the other tospoviruses that are known to occur in India. This is the first report of a comparison of complete sequences of M RNA of WBNV.

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Acknowledgments

Financial support from the Department of Biotechnology, Govt. of India, and Indian Agricultural Research Institute, New Delhi, is thankfully acknowledged.

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Authors and Affiliations

  1. Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India

    Rakesh Kumar, B. Mandal, A. S. Geetanjali & R. K. Jain

  2. Advanced Centre for Biotechnology, M. D. University, Rohtak, 124001, India

    P. K. Jaiwal

Authors
  1. Rakesh Kumar
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  2. B. Mandal
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  3. A. S. Geetanjali
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  4. R. K. Jain
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  5. P. K. Jaiwal
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Corresponding author

Correspondence to B. Mandal.

Additional information

The sequence reported here is available in GenBank under the accession number GU474545.

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705_2010_687_MOESM1_ESM.tif

Comparison of genome organisation of the medium RNA of watermelon bud necrosis virus (WBNV) isolate-wDel, -Wm-Som and groundnut bud necrosis virus (GBNV). The shaded box represents the NSm open reading frame (ORF), and the open box represents the Gn/Gc ORF. IGR intergenic region. Vertical solid lines indicate N-glycosyltion sites, and dotted vertical lines indicate O-glycosylation sites. Hatched vertical boxes indicate transmembrane domains. The open triangle represents the cleavage site VYL-LN, and the solid triangle represents the cleavage site PSSIA-LK. Arrows indicate the direction of the ORF and the sizes of the proteins. The scale (1–4,801) at the top indicates nucleotide positions. (TIFF 769 kb)

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Kumar, R., Mandal, B., Geetanjali, A.S. et al. Genome organisation and sequence comparison suggest intraspecies incongruence in M RNA of Watermelon bud necrosis virus. Arch Virol 155, 1361–1365 (2010). https://doi.org/10.1007/s00705-010-0687-z

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