Bean common mosaic virus -BCMV- is an important plant pathogen causing considerable economic loss to legume production worldwide. In this study, the molecular characterizations of four BCMV isolates from Iran were determined, and their genetic variation and phylogenetic relationship compared with those of 49 other from GenBank. The genome contained a single open reading frame encoding a polyprotein of 3221, 3222, 3201 and 3202 amino acids -aa- in Ir-MSC1, Ir-GoB, Ir-MJB, and Ir-MSC2, respectively. Phylogenetic analysis of the polyprotein nucleotide sequences revealed that all 53 BCMV isolates clustered into six phylogroups distinguishable according to their genetic distances, namely S -soybean-, P -peanut-, C -common bean- and also three other distinct groups -R1, R2, and R3- of isolates all of which were recombinant. Iranian BCMV isolates did not form a compact group in the phylogenetic trees and shared 82.7–97.0% nt and 98.6–98.9% aa sequence identity among themselves and 80.1–98.7% nt and 83.4–99.8% aa sequence identity with the 49 other BCMV isolates. Of the 53 BCMV isolates studied, 34 -including Ir-MSC1 and Ir-GoB- were found to be recombinants at multiple regions of the genomes. The 19 non-recombinant isolates fell into three main phylogroups -S, P, and C- and tended to be classified according to their original host -with some exceptions-. Statistically highly significant genetic differentiation -FST > 0.80- and infrequent gene flow were detected between the three phylogroups, suggesting ancestral differentiation. The normalized values for dN-dS indicated different purifying selection pressures acting on each of cistrons, with the P1 and NIa-Pro being subjected to the weakest and strongest functional constraints, respectively. Some codons -mainly in P1 and P3 regions- were under positive selection. This study presents a comprehensive analysis of evolutionary forces shaping the genetic structure of BCMV with implications for international exchanges of propagating materials.

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