I agree with Pieter that life finds a way.
-- But watching it from another perspective... If you have an apple tree, all it's sexual offspring will have significantly different genomes. Maternal and paternal DNA mix, recombine, holiday junction, transposon, retorotransposons, rearrangements, gene deletion, gene duplication, mutation, .... Nature is crazily recombining.
Now look at a field, millions of e.g. bellis perennis, each with different genomes. None is the same. Though also non of them becomes really a superweed. It is pretty paranoid to believe if you add GFP or a heavy-metal methylating enzyme will make it a superweed. It is just another recombinant (natural recombinants and unnatural recombinants included) plant.
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