The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Abstract

<i>Rehmannia</i> is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six <i>Rehmannia</i> species using Illumina sequencing technology to elucidate the interspecific variations. <i>Rehmannia</i> plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (<i>rpoA</i>, <i>rpoC2</i>, <i>accD</i>) have potentially experienced positive selection. Plastome size variation of <i>Rehmannia</i> was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in <i>Rehmannia</i> plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that <i>Rehmannia</i> was monophyletic and sister to the clade of <i>Lindenbergia</i> and the parasitic taxa in Orobanchaceae. The interspecific relationships within <i>Rehmannia</i> were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of <i>Rehmannia</i>.