Multiplex PCR and genome analysis of Carnation mottle virus Indian isolate.

The complete nucleotide sequence of an Indian isolate of Carnation mottle virus (CarMV) was determined to be 4005 bp in length, 2 bp longer than previous reports. The viral genome was amplified by RT–PCR using primers covering the entire genome length. Coat protein (CP) and movement protein (MP) genes were also amplified by multiplex RT–PCR from annual and perennial carnations. Identity of the amplified products was verified by sequencing. CP and MP genes of four Indian isolates were compared with the available sequences in the GenBank database. CP gene of annual and perennial carnations showed high similarity (95– 100%) compared to isolates reported from different parts of the world. MP genes (p7 and p9) showed 95– 98% nucleotide similarity while at the amino acid level similarity, of 86–98% for p7 and 92–98% for p9 respectively, was obtained. Recombination detection analysis indicated recombination in an isolate from annual carnation and division of CarMV isolates into six groups on the basis of recombination analysis