Molecular characterization of two sugarcane streak mosaic virus isolates from Iran with emphasis on its population structure.

Sugarcane streak mosaic virus (SCSMV; the genus Poacevirus, the family Potyviridae) is an economically important causal agent of sugarcane mosaic disease in Asia. In this study, for the first time, we determined the complete genomic sequences of two Iranian SCSMV isolates, IR-Khuz6 and IR-Khuz57 from sugarcane. The sequences of both isolates were 9,782 nucleotides (nt) long, excluding the 3' poly(A) tail. Both of them contained a 5'-untranslated region (UTR) of 199 nt, an open reading frame of 9,393 nt encoding a polyprotein of 3,130 amino acids (aa), and 3'-UTR of 190 nt. SCSMV-IR-Khuz6 and IR-Khuz57 genome nucleotide sequences were in 97.7% identical and shared identities of 81-92.4% with 10 other SCSMV isolates available in the GenBank. The highest identity was shared with the isolate PAK (NC_014037) from Pakistan. When separate genes were compared, most of the genes shared the highest identities with Pakistani isolate. Phylogenetic analysis of the complete genomic nucleotide and polyprotein amino acid sequences reveals that all SCSMV isolates clustered into two main groups. Both IR-Khuz6 and IR-Khuz57 clustered with isolates from Pakistan (PAK) and India (IND671) in group II but formed a separate subgroup. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. The results indicate that gene flow and selection pressure are important evolutionary factors shaping the genetic structure of SCSMV populations with implications for global exchange of sugarcane germplasm.