Sugarcane (Saccharum officinarum) and maize (Zea mays) are of the strategic plants belonging to Gramineae family that possess economic, nutritional and medicinal importance. Sugarcane mosaic virus (SCMV) is one of the major limiting factors in sugarcane and maize production and can cause serious crop losses throughout the world. In the absence of complete genomic sequence of potyviruses, CI-coding region are the most suitable for diagnostic and taxonomy purposes. Two SCMV isolates, NRA and ZRA, from sugarcane and maize plantation in Mazandaran were subjected to RT-PCR using potyvirus degenerate primers corresponding to the virus CI gene. Expected PCR products of 680bp were cloned and sequenced. Phylogenetic tree based on multiple sequence alignment of 680 nt of CI gene divided all SCMV isolates into four groups. Iranian SCMV isolates were classified in the group II with isolates from Argentina and Australia. Phylogenetic analysis showed that Iranian isolates share 77.4%-97.2% nucleotide sequence identity and 94.3%-100% amino acid sequence identity with other isolates of SCMV recorded in GenBank. Iranian SCMV-NRA and -ZRA isolates showed the highest nucleotide sequence (97.2%, 95.7%) and amino acid sequence (100%) identity with ARG-915 isolate from Argentina. This is the first report of SCMV detection and classification based on CI gene in Iran.
