Recombination in single-stranded RNA viruses is one of the principal mechanisms responsible for their evolution. Here we show, using a variety of different methods, that the 3' untranslated region (3'UTR) of subgroup II strains of cucumber mosaic virus [CMV(II)] is related more closely to that of tomato aspermy virus (TAV) than to those of CMV(I) strains. These results suggest that the CMV(II) 3'UTR arose by interspecific CMV/TAV recombination. The putative crossover is close to the 5' end of the 3'UTR, at a recombination hot spot previously observed in short time-frame experiments. The CMV(II) strains show divergence from TAV at specific points along the 3'UTR that most probably indicate adaptive changes due to natural selection. Thus, for the large majority of CMV(II) strains examined, the 3'UTR has two discrete regions, W (nt 1902-1971) and Y (nt 2126-2184), that are more similar to the corresponding regions of TAV than to those of CMV(I) strains.
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