Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks.

Although we observed a marginally significant tendency for breakpoints to cluster at sites where TOX had a strongly predicted secondary structure but TYX did not ( p = 0.0579; Table S2 ), it is important to stress that we performed three separate tests and that we would have expected an approximately one in six chance of finding at least one p -value this close to significance even in the absence of any real associations.

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Irrespective of the window size used in these permutation based recombination hot- and cold-spot tests, a single highly significant recombination hot-spot was apparent in the IR around the origin of virion strand replication.

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