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Genomic sequence analysis of four new chrysanthemum virus B isolates: evidence of RNA recombination

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Abstract

Chrysanthemums worldwide suffer from a high incidence of infection with chrysanthemum virus B (CVB), a member of the genus Carlavirus, family Betaflexiviridae. Three major lineages or strains of this virus have been found in India, but none have been characterized beyond the genetic variation they display in their coat protein genes. Here, we describe the analysis of four near-complete genome sequences (from the three lineages) representing the genetic diversity of these strains. Ranging in size from 8815 to 8855 nucleotides (excluding the polyA tail), these four isolates have a genome organization very similar to that of the recently reported Japanese isolate of CVB, with which they share between 70 and 73% genome-wide sequence identity. We present further evidence that recombination may feature quite prominently in the evolution of CVB.

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Acknowledgments

The authors are thankful to the Director, Council of Scientific and Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India, for providing the necessary facilities to carry out the work, and to Digvijay Singh for technical help with nucleotide sequencing. A fellowship to LS and financial support from the Department of Biotechnology, Govt. of India, and Council of Scientific and Industrial Research are duly acknowledged. This is IHBT publication number: 2206.

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Authors and Affiliations

  1. Plant Virus Laboratory, Council of Scientific and Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India

    Lakhmir Singh, Vipin Hallan, Raja Ram & A. A. Zaidi

  2. Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa

    D. P. Martin

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  1. Lakhmir Singh
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  2. Vipin Hallan
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  4. Raja Ram
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Corresponding author

Correspondence to Vipin Hallan.

Electronic supplementary material

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705_2011_1190_MOESM1_ESM.doc

Supplementary Fig. 1 ClustalW multiple alignment of the complete genomes of five CVB isolates. Sequences in green boxes represent initiation codons, and those in red boxes, stop codons (DOC 170 kb)

705_2011_1190_MOESM2_ESM.doc

Supplementary Fig. 2 ClustalW multiple alignment of the replicase, TGB1, TGB2, TGB3, CP and NABP protein sequences from five CVB isolates. Conserved motifs are indicated by green shading (DOC 77 kb)

Supplementary Fig. 3 (JPEG 95.6 kb)

705_2011_1190_MOESM4_ESM.doc

Supplementary Fig. 4 Mechanical inoculation of various CVB isolates on Petunia hybrida, showing variation in biological reaction. a Mottling induced by CVB-UK. b Narrowing of leaf lamina induced by CVB-TN. c Leaf deformation induced by CVB-UP. d Mosaic induced by CVB-AR (partially sequenced isolate of CVB Arunachal Pradesh 109287621). e Mosaic puckering induced by CVB-PB (DOC 1155 kb)

Supplementary Table 1 (DOC 53 kb)

Supplementary Table 2 (DOC 47 kb)

Supplementary Table 3 (DOC 28 kb)

Supplementary Table 4 (DOC 57 kb)

Supplementary Table 5 (DOC 45 kb)

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Singh, L., Hallan, V., Martin, D.P. et al. Genomic sequence analysis of four new chrysanthemum virus B isolates: evidence of RNA recombination. Arch Virol 157, 531–537 (2012). https://doi.org/10.1007/s00705-011-1190-x

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