I'd been tried CTAB method for this fungi many times but it gave my heavy RNA and unclear DNA bands, I don't know what is the problem and its solution.. so what is the best used kit for extraction?
Not gonna do any advertisement here but, I am also using CTAB DTAB method and yes it was sometimes disappointing.
But several question first.
1. Have you ever use NanoDrop to measure the DNA concentration?
2. Is the DNA purified?
3. How about the primers? Are they good enough or maybe there is any error in primer making? Such as primer dimer?
4. Have you optimizing the annelaing temperature when doing the PCR?
Maybe these questions will help you as well, means it might lead you to the errors you had.
Speaking of which, there are any genome extraction kit. If you have some budget, try Purelink DNA and or RNA kit (not advertising) but I did my research several years before, the result was good.
Then purify your DNA target. Sometimes any impurity will give you bad result in amplification and electrophoresis.
Too much or too less DNA concentration also give you bad result in PCR amplofication, thats why I suggest you to use nanodrop.
Maybe we could discuss any further. Bcs there are less clues about your question.
you can used manual method for extraction isoprobanol , cloroform, EDTA method then digest the product with RNAse to make sure that the RNA are absent good luck for you