title: Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potexviruses.
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.
authors.affiliation: Plant Virology Lab, Floriculture Division, Institute of Himalayan Bioresource Technology (CSIR), Post Box No. 6, Palampur 176 061, India.
authors.forename: Ang Rinzing
authors.initials: AR
authors.lastname: Sherpa
authors.forename: Vipin
authors.initials: V
authors.lastname: Hallan
authors.forename: Promila
authors.initials: P
authors.lastname: Pathak
authors.forename: Aijaz Asghar
authors.initials: AA
authors.lastname: Zaidi
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D016679:Genome, Viral; D009029:Mosaic Viruses / Q000235:genetics*; D016366:Open Reading Frames; D017863:Potexvirus / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers