*4.2. Organellar Genome Sequencing, Assembly and Annotation*

Sequence libraries were quantified using Bioanalyzer 2100 (Agilent, CA, USA). The paired-end libraries were prepared using Illumina library preparation manufacturer's protocol, and genomic DNA of 2 × 100 bp and insert size of ~200 bp was sequenced using Illumina MiSeq platform (Illumina, San Diego, CA, USA)

The produced paired-end reads filtered for adapters, low-quality bases (Phred score Q > 24) and size (length cutoff for 50 bp), and possible contaminants using Trimmomatic v. 0.38 [56]. The resulting paired-end reads were mapped in the search for discarding mitochondria and nuclear reads with Bowtie2 v.2.2.3 [57] using very sensitive local and -N 1 parameters and *Utricularia* spp. (NC\_021449, KY025562, and KT336489) chloroplasts as reference genomes. The resulting reads were assembled using SPAdes v. 3.7.1 [58] and regions with assembly uncertainties were extended using iterative read mapping performed using MITObim v.1.8 [59].

The organelles genomes were primarily annotated using DOGMA [60], cross checked with GeSeq [61], and start and stop codons were adjusted manually for annotation refinements. The tRNAs were annotated using tRNA-scan [62], implemented in DOGMA and Aragorn [63]. The rRNAs were annotated using RNAmmer and BLASTn searches with available *Utricularia* cpDNA genomes. The cp genome map was constructed using the Organellar Genome Draw program [64].

#### *4.3. Repeats and SSR Analyses*

To avoid redundant results, only one IR of each *Utricularia amethystina* cpDNA was used and direct, forward, reverse, and palindromic repeats were identified using REPuter [65] with a minimal size of 30 pb and Hamming distance of 3. Simple sequence repeats (SSR) were detected using MISA-web [66]

by setting the minimum number of repeats to 7, 4, 4, 3, 3, and 3, for mono-, di-, tri-, tetra-, penta-, and hexanucleotides, respectively.
