*2.6. RNA Edit*

The RNA editing analyses were carried out using the PREPACT3 tool, and in-house script to search for validation of editing sites using RNA-Seq mapped reads. The PREPACT3 predicted 154 sites for *U. amethystina* purple, 140 for *U. amethystina* white, and 146 for *U. amethystina* yellow. Most amino acid changes are shared between populations, and comparison between *Utricularia amethystina* morphotypes showed 22 genes with the same editing sites and 15 genes with differences in the quantity and amino acid composition changes (for more information see Supplementary Tables S8–S10). According to the results, there are 13 types of amino acid transitions in the three *U. amethystina*. The most prevalent nonsynonymous substitutional changes occurred between Alanine to Valine and Serine to Leucine, followed by Leucine to Phenylalanine, Proline to Serine, Threonine to Isoleucine, Serine to Phenylalanine, Proline to Leucine, Histidine to Tyrosine, Threonine to Methionine, Proline to Phenylalanine, Arginine to Cysteine, Glutamine to Stop codon, and Arginine to Tryptophan (Figure 8). For RNA-Seq-based results, only three nonsynonymous amino acid substitutions were found (Figure 8; Table 2).

**Figure 8.** Quantities of amino acid changes from the prediction and RNA-Seq data of RNA-editing sites for each *Utricularia amethystina* morphotype. Purple, yellow, and gray bars denote *U. amethystina* purple, yellow, and white morphotypes, respectively.

The results from RNA-Seq data showed eight nonsynonymous and eight synonymous sites for the three *U. amethystina* morphotypes. Regarding nonsynonymous sites, *U. amethystina* purple and yellow have *rps*14 and *pet*B genes edition, and for *U. amethystina* white, edition sites were two in *rps*14, *pet*B, and *ndh*B (Table 2). The same edited sites in the same gene position were found in *pet*B for all *U. amethystina* samples. In addition, the *rps*14 gene from purple is the same as *rps*14 in position 36,572 for white, and *rps*14 gene from yellow is the same as the *rps*14 in position 36,497 for white.


**Table 2.** RNA editing sites predicted using RNAseq data in *Utricularia amethystina* cpDNA. The editing level is given in percentage and is showed for each biological replicate. \* denotes amino acids with a change in physicochemical composition.
