Good day,

I assembled a mitochondrial genome using GetOrganelle, which produced a single circular genome. When I annotated it with MFANNOT, the output stated: “cox1 may be either split by linearization of a circular-mapping genome, or it is trans-spliced (annotation in comments).”

Upon examining the sequence, I found that the region in question was located at the very end of the FASTA file. My question is whether it is appropriate/legal to simply move this terminal sequence to the beginning—effectively rotating the genome (Cut/paste). I attempted this adjustment and, after re‑annotating with MFANNOT, cox1 was predicted as a complete gene and could be visualized in OGDraw.