Abstract
RNA recombination is one of the two major factors that create RNA genome variability. Assessing its incidence in plant RNA viruses helps understand the formation of new isolates and evaluate the effectiveness of crop protection strategies. To search for recombination in Soybean mosaic virus (SMV), the causal agent of a worldwide seed-borne, aphid-transmitted viral soybean disease, we obtained all full-length genome sequences of SMV as well as partial sequences encoding the N-terminal most (P1 protease) and the C-terminal most (capsid protein; CP) viral protein. The sequences were analyzed for possible recombination events using a variety of automatic and manual recombination detection and verification approaches. Automatic scanning identified 3, 10, and 17 recombination sites in the P1, CP, and full-length sequences, respectively. Manual analyses confirmed 10 recombination sites in three full-length SMV sequences. To our knowledge, this is the first report of recombination between distinct SMV pathotypes. These data imply that different SMV pathotypes can simultaneously infect a host cell and exchange genetic materials through recombination. The high incidence of SMV recombination suggests that recombination plays an important role in SMV evolution. Obtaining additional full-length sequences will help elucidate this role.
Highlights
Soybean mosaic virus (SMV) is found in all soybean-growing regions of the world
In the United States, at least 98 SMV isolates have been documented [7,8]. Based on their differential interactions with SMV resistant cultivars, these isolates are classified into seven distinct strain groups, G1 through G7 [7,8]
In accordance with the parsimony principle, we have presented the output that explains the relationships between SMV sequences in all alignments by the smallest number of recombination events (Figure 1B) [Additional file 2]
Summary
Soybean mosaic virus (SMV) is a member of the genus Potyvirus, the family Potyviridae. Similarity patterns and phylogenetic trees constructed for the sequence alignment regions demarcated by the recombination sites confirmed two recombination events in each of the isolates: 'w' and 'x' in G5 and 'y' and 'z' in G7H (Figure 2) [Additional file 3] [Additional file 4]. The same SH score of 0 was obtained when the tree topologies for the regions from the beginning of the sequence alignment to 'w' and from 'z' to end of the sequence alignment were tested against sequence alignments between the recombination sites These results indicated that the different topologies cannot substitute for each other in explaining the variability of SMV sequences between G5 and G7H recombination sites that we identified. The high frequency of recombination detected in SMV suggests that recombination plays an important role in SMV evolution and this should be considered when novel antiviral strategies are developed
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