Other than most of it, including the "wind up" part. And, how messed up does a plant's genome need to be to prevent you from easily sequencing the whole thing?

Other than most of it, including the "wind up" part. And, how messed up does a plant's genome need to be to prevent you from easily sequencing the whole thing? How do the companies in the book keep a base sequence for the unmodified plant secret? Because if they don't, you can align the partial sequences from the modified version to that, making the modified version very easy and cheap to sequence.