*Article* **Intraspecific Variation within the** *Utricularia amethystina* **Species Morphotypes Based on Chloroplast Genomes**

**Saura R. Silva 1,\*, Daniel G. Pinheiro 1, Helen A. Penha 1, Bartosz J. Płachno 2, Todd P. Michael 3, Elliott J. Meer 4, Vitor F. O. Miranda 5,\* and Alessandro M. Varani 1,\***


Received: 18 October 2019; Accepted: 27 November 2019; Published: 5 December 2019

**Abstract:** *Utricularia amethystina* Salzm. ex A.St.-Hil. & Girard (Lentibulariacea*e*) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three *U. amethystina* morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three *U. amethystina* morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the *psb*M and *pet*N genes in *U. amethystina* yellow. Phylogenetic analyses indicate that *U. amethystina* morphotypes are monophyletic. Furthermore, in contrast to the terrestrial *Utricularia reniformis* cpDNA, the *U. amethystina* morphotypes retain all the plastid NAD(P)H-dehydrogenase (*ndh*) complex genes. This observation supports the hypothesis that the *ndh*s in terrestrial *Utricularia* were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of *Utricularia ndh*s gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., *rps14* and *petB*). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.

**Keywords:** *Utricularia amethystina*; Lentibulariaceae; chloroplast phylogenomics; organelle genome; carnivorous plants; polymorphic species; intraspecific variation; *ndh* genes
