Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Abstract

<i>Papaver rhoeas</i> L. and <i>P. orientale</i> L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of <i>P. rhoeas</i> and <i>P. orientale</i> are reported. Results show that the complete chloroplast genomes of <i>P. rhoeas</i> and <i>P. orientale</i> have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three <i>Papaver</i> species. These differences include the <i>ycf1</i> gene and intergenic regions, such as <i>rpoB-trnC</i>, <i>trnD-trnT</i>, <i>petA-psbJ</i>, <i>psbE-petL</i>, and <i>ccsA-ndhD</i>. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of <i>Papaver</i> species and will benefit further investigations of these species.