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Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potexviruses

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Abstract

The complete nucleotide sequence of an Indian strain of Cymbidium mosaic virus (CymMV) was determined and compared with other potexviruses. Phylogenetic analyses on the basis of RNA-dependent RNA polymerase (RdRp), triple gene block protein and coat protein (CP) amino acid sequences revealed that CymMV is closely related to the Narcissus mosaic virus (NMV), Scallion virus X (SVX), Pepino mosaic virus (PepMV) and Potato aucuba mosaic virus (PAMV). Different sets of primers were used for the amplification of different regions of the genome through RT-PCR and the amplified genes were cloned in a suitable vector. The full genome of the Indian isolate of CymMV from Phaius tankervilliae shares 96–97% similarity with isolates reported from other countries. It was found that the CP gene of CymMV shares a high similarity with each other and other potexviruses. One of the Indian isolates seems to be a recombinant formed by the intermolecular recombination of two other CymMV isolates. The phylogenetic analyses, Recombination Detection Program (RDP2) analyses and sequence alignment survey provided evidence for the occurrence of a recombination between an Indian isolate (AM055720) as the major parent, and a Korean type-2 isolate (AF016914) as the minor parent. Recombination was also observed between a Singapore isolate (U62963) as the major parent, and a Taiwan CymMV (AY571289) as the minor parent.

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Abbreviations

BAMV:

Bamboo mosaic virus

ClYMV:

Clover yellow mosaic virus

CP:

coat protein

CsCMV:

Cassava common mosaic virus

CVX:

Cactus virus X

CymMV:

Cymbidium mosaic virus

FoMV:

Foxtail mosaic virus

LVX:

Lily virus X

NCR:

non-coding protein

NMV:

Narcissus mosaic virus

ORF:

open reading frame

ORSV:

Odontoglossum ringspot tobamovirus

RDP2:

Recombination Detection Program

RdRp:

RNA-dependent RNA polymerase

PAMV:

Potato aucuba mosaic virus

PapMV:

Papaya mosaic virus

PepMV:

Pepino mosaic virus

PlAMV:

Plantago asiatica mosaic virus

PVX:

Potato mosaic virus

SMYEV:

Strawberry mild yellow edge virus

SVX:

Scallion virus X

TGB:

triple gene block

WClMV:

White clover mosaic virus

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Authors and Affiliations

  1. Plant Virology Lab, Floriculture Division, Institute of Himalayan Bioresource Technology (CSIR), Post Box # 6, Palampur, 176 061, India

    Ang Rinzing Sherpa, Vipin Hallan & Aijaz Asghar Zaidi

  2. Botany Department, Panjab University, Chandigarh, 160 014, India

    Promila Pathak

Authors
  1. Ang Rinzing Sherpa
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  2. Vipin Hallan
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  3. Promila Pathak
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  4. Aijaz Asghar Zaidi
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Correspondence to Aijaz Asghar Zaidi.

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Sherpa, A.R., Hallan, V., Pathak, P. et al. Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potexviruses. J Biosci 32, 663–669 (2007). https://doi.org/10.1007/s12038-007-0066-4

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  • DOI: https://doi.org/10.1007/s12038-007-0066-4

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