*2.4. Intraspecific Comparison: Species Polymorphism*

The nucleotide diversity (π) analyses indicated that the IRs exhibited lower variability than LSC and SSC regions (Figure 6). There are twelve spots of chloroplast genome regions that showed remarkably higher π values (>0.02), including nine gene (*trn*H, *psb*A, *trn*C, *pet*N, *psb*M, *trn*D, *psa*A, *ycf* 4 and *ndh*F) and 12 intergenic regions (*trn*H-*psb*A, *rps*16-*trn*Q, *trn*C-*pet*N, *rpo*B-*trn*C, *pet*N-*psb*M, *trn*C-*pet*N, *psb*M-*trn*D, *trn*D-*trn*Y, *psa*A-*ycf* 3, *ycf* 3-*trn*S, *psa*I-*ycf* 4, *ndh*F-*rpl*32). (More details in Supplementary Table S6.)

**Figure 4.** mVISTA identity plot based in Shuffle-LAGAN alignment for *Utricularia amethystina* morphotypes and previously reported chloroplasts of other *Utricularia* species. *U. amethystina* purple was used as a reference. NCS denotes non-coding sequence.

**Figure 5.** Boundaries between SSC regions of all previously published *Utricularia* species. cpDNA regions color denote different chloroplast gene families.

**Figure 6.** Nucleotide diversity (π) for the three *Utricularia amethystina* morphotypes. Each blue dot represents the nucleotide diversity per 500 bp. Orange dots denote the nucleotide diversity for the un-inverted region in *U. amethystina* yellow (*psb*M-*pet*N).
