I've been having a similar issue with sequencing clones in a pET vector. Since the sequence of the vector alone and PCR products come back fine, Genewiz tells me that the issue might be that the bacteria (Top10 E. coli) are manipulating the DNA to avoid a toxic product. Weird.
I had the same problem and it turned out to be a transformation issue (we were using an old electroporator). Try starting fresh with your transformations and pick the most robust (biggest colonies) from your YPDS plates to inoculate in MGY O/N. We picked colonies after 4 day incubations at 30 degrees.
Update: for whatever reason, we figured out that our Pichia strains (X33 and GS115) would not grow in generic YNB, only Invitrogen's YNB. Very frustrating! Unfortunately, the cultures are still not very strong, but I plan to try a few other conditions to improve their strength.
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