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

Abstract

<i>Utricularia amethystina</i> Salzm. ex A.St.-Hil. & Girard (Lentibulariacea<i>e</i>) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three <i>U. amethystina</i> 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 <i>U. amethystina</i> 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 <i>psb</i>M and <i>pet</i>N genes in <i>U. amethystina</i> yellow. Phylogenetic analyses indicate that <i>U. amethystina</i> morphotypes are monophyletic. Furthermore, in contrast to the terrestrial <i>Utricularia reniformis</i> cpDNA, the <i>U. amethystina</i> morphotypes retain all the plastid NAD(P)H-dehydrogenase (<i>ndh</i>) complex genes. This observation supports the hypothesis that the <i>ndh</i>s in terrestrial <i>Utricularia</i> were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of <i>Utricularia</i> <i>ndh</i>s gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., <i>rps14</i> and <i>petB</i>). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.