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Genome structure and sequence are notably conserved between members of the family Potyviridae. However, some genomic regions of these viruses, such as that encoding the P1 protein, show strikingly high variability. In this study, some partially conserved motifs were identified upstream of the quite well-conserved protease domain located near the P1 C terminus. The irregular distribution of these motifs suggests that the potyviral P1 proteins have undergone complex evolutionary diversification. Evidence was found of recombination events in the P1 N-terminal region, similar to those reported in potyviruses of the bean common mosaic virus subgroup, but also affecting other potyviruses. Moreover, intergeneric recombination events affecting potyviruses and ipomoviruses were also observed. Evidence that these recombination events could be linked to host adaptation is provided. Specific sequence features and differences in net charge help to classify the P1 proteins of members of the family Potyviridae into two groups: those from potyviruses and rymoviruses and those from tritimoviruses. The ipomovirus Cucumber vein yellowing virus has two P1 copies arranged in tandem, the most N-terminal one being of the potyvirus type and the other being of the tritimovirus type. These findings suggest that both recombination and gene duplication have contributed to P1 evolution and helped to facilitate successful adaptation of members of the family Potyviridae to a wide range of host species.

Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae