Hello Marco,

RNAseq is a technique for determining expression patterns, not precisely genomic comparisons. I assume the two RNAseq dataset that you have come from the same tissue (leaves, xylem, etc) in both cases. Then I think you will be able to establish if the tissues in both geographically separated plants express the same proteins. In that case, when you lack a genome, you will have to obtain profiles of proteins from the RNA sequences in both datasets. Then you can compare those profiles and say, for example that one dataset have higher relative numbers of certain category of proteins than in the other and so on. You can use a reference protein database such as Pfam, UniProt or Kegg to generate the profiles and the sequence comparison with tools like BLASTX or DIAMOND/blastx.

I hope that helps. Best regards.

Hi Marco

I thing that you can compare with free-aligment based method, we used one of them to compares genomic shotgun sequences of different tomatoes cp , see https://peerj.com/preprints/3271/