**1. Introduction**

The species of the carnivorous plant family Lentibulariaceae are grouped in three genera: *Pinguicula* L., *Genlisea* A.St-Hil., and *Utricularia* L. [1,2], and are increasingly becoming important plant models mainly due to their alternative nutrient uptake system, their morphological non-orthodox body structure, characterized by Fuzzy Arberian Morphology [3,4], and particular genomic characteristics, such as high mutational levels with nuclear genome shrinkage and expansion in some lineages [5,6].

*Utricularia* is the biggest genus and most widespread group of carnivorous plants and is very diverse regarding its distribution and habit (e.g., terrestrial, aquatic, lithophytes, epiphytes, and reophytes) [7]. Moreover, several species are polymorphic, which may lead to controversial taxonomic classification. For instance, *Utricularia amethystina* Salzm. ex A.St.-Hil. & Girard is a terrestrial herb, with petiolate and rosetted leaves. The species is broadly distributed in about 18 different countries of the tropical and subtropical America [7], commonly found in different altitudes (from inselbergs in the Guianas [8] to the coast of Brazil [9]) and habitats such as humid sandy soil of the savannas, swamps, and soil between rocks usually near streams, rivers, and waterfalls.

The species is classified in the *Utricularia* sect. *Foliosa* Kamie ´nski, showing common morphological characteristics making it easy to distinguish from other *Utricularia* sections due to its connate bracts and bracteoles, which is the singular morphology of utricles (carnivorous traps), and the capsule dorsoventrally and bivalvate dehiscence. However, the distinction between the conspecific species is not a trivial task, as *U. amethystina* shows high intraspecific variation, mainly between reproductive characters, such as the corolla shapes and colors, which can vary from shades of purple (Figure 1A), white (Figure 1B) to yellow (Figure 1C) [7].

**Figure 1.** *Utricularia amethystina* species morphotypes are differentiated mainly by corolla color. (**A**) *U. amethystina* purple morphotype; (**B**) *U. amethystina* white morphotype; (**C**) *U. amethystina* yellow morphotype.

This intraspecific morphological variation resulted in several taxonomic rearrangements since the earliest descriptions at nineteenth century [10,11] and even now there is much controversy about if the species is one or more [12,13]. Taylor (1989) [7] struggled to separate the species based on reproductive characters, such as corolla shape, pedicel sizes, palynological characters, and calyx indumentum, but he couldn't find traits for enough taxonomical circumscriptions to split the different morphotypes. Indeed, in his *Utricularia* taxonomic monograph, he synonymized 31 taxa under the binomial "*Utricularia amethystina*" and he wrote "*U. amethystina* is a most 'difficult' and excessively polymorphic species..." (Taylor, 1989 [7], p. 291). Therefore, he assumed one name for the species, as he was unable to find discontinuities to support taxa separation due to the high degree of polymorphism between populations. However, to date, there is no proper taxonomic treatment to solve this question. In addition, only a few genetic differences have been explored [13], such as the chloroplast regions *rps*16, *trn*L-F, *trn*D-T, and nuclear ITS, but these markers were not able to give enough resolution to distinguish them all. In this context, chloroplast genomes are a valuable resource for phylogenies, and the study of their structure and content can provide clues for improving inter- and intraspecific studies, such as population biology [14], and even the discovery of new species [15].

The chloroplast genomes of most angiosperms have conserved quadripartite structure separated in Large and Small Single Copy regions (LSC and SSC, respectively) and two inverted repetitive regions (IRs) [16]. However, comparative analyses indicate that some plants, such as parasitic [17], mycoheterotrophic (e.g., in [18,19]), and species of carnivorous plants from the order Caryophyllales [20,21], have suffered substantial rearrangement and gene losses throughout plant evolution. For example, across diverse lineages of plants, chloroplast genomes lack NAD(P)H-dehydrogenase (*ndh*) complex genes, genes that could have been involved in the transition from aquatic to terrestrial habit thought plant evolutionary history [22,23].

Within Lentibulariaceae family, there are published chloroplast genomes (cpDNA) of *Pinguicula ehlersiae* [24] and seven *Genlisea* species [24,25]. There are cpDNA genomes available for four *Utricularia* species: *U. gibba* [26], *U. macrorhiza* [24], *U. reniformis* [27], and *U. foliosa* [28].

All published *Utricularia* cpDNAs have the typical quadripartite structure and the same genes as most angiosperms. However, some species exhibit variation, such as two complete copies of *ycf* 1 and *ndh*F in *U. gibba*, and *U. reniformis*, which has reduced chloroplast size due to several losses in all *ndh*s genes repertoire that could not be integrally found either in the mitochondrial genome [29] nor in the nuclear DNA (unpublished data). Indeed, *U. reniformis* is a terrestrial species and other assessed *Utricularia* are aquatic, and based on this observation, Silva et al. (2016) proposed that the loss of *ndh*s could be related to terrestrial habit [27]. Nonetheless, other studies are still needed for a better understanding of genes especially the evolution of the *ndh* genes in the genus.

Herein, we present the chloroplast genomes of three *Utricularia amethystina* morphotypes to assess inter- and intraspecific sequence variability and polymorphic regions that could be used for further phylogenetic studies. In addition, we employed chloroplast transcriptome to assess gene expression and identify the RNA editing sites in each chloroplast. We also compare *ndh* gene gains and losses across the sequenced *Utricularia* cpDNA species, to examine the variation of structural changes across the genus.
