Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination

Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26 %) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the Cl/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5′) region of GC-rich and downstream (3′) region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.