I'm working on a plant species without a reference genome, I do have transcriptome data available (de-novo assembly). Now I want to do qPCR on a group of genes that were differentially expressed in the transcriptome, BUT I run into a problem.

I have DNA contamination that causes a band in my -RT. I tried different DNases (Turbo) but those degrade my RNA. I cannot design exon spanning primers because I do not have a genome reference available. Even genome references of closely related species are lacking at this point.

How do I go from here?