The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Abstract

Rehmannia 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 Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia 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 (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia 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 Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia.

Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales

“…Such conservatism is expected considering the low substitution rate in chloroplasts and the presumed recent age of divergence among them. Similar findings have also been detected in many other closely related taxa, such as genera or tribes (Choi et al, ; Huang et al, ; Kaila et al, ; Yang et al, ; Li et al, ; Zeng et al, ).…”

Plastomes of nine hornbeams and phylogenetic implications

“…It should be noted that we obtained identical topological relationships using the whole plastomes or noncoding datasets. However, results based solely on the coding genes suggested different phylogenetic positions for C. betulus and C. caroliniana (Figure ), presumably because the whole plastome and noncoding datasets provided more detailed signals for these two species (Hu et al., ; Zeng et al., ). These findings suggest that it is essential to assess the consistency of phylogenetic relationships based on whole plastomes and both their coding and noncoding regions, as well as their correspondence to phylogenies derived from analyses of nuclear genes or genomes.…”

“…Poor phylogenetic resolution and inconsistency of gene trees are major complications when attempting to construct trees of life for various groups of organisms, as illustrated by numerous authors (e.g., Mallet, Besansky, & Hahn, ; Ren, Conti, & Salamin, ; Xu, Wu, Gao, & Zhang, ; Zeng et al., ; Zhang & Li, ). In this study, we addressed these issues in analyses of the genus Carpinus L. (hornbeams), subfamily Coryloideae, of the Betulaceae.…”

“…For example, Zeng et al. () used whole plastome sequences and coding genes to construct phylogenetic trees of Rehmannia , both of which indicated four nearly identical clades and had high levels of phylogenetic resolution. The noncoding regions in a plastome usually have higher variation rates than the coding genes (Hu et al., ; Zhang & Li, ).…”

“…With the development of high-throughput sequencing technology, it is becoming much cheaper and easier to sequence whole plastomes of plants (Hu et al, 2016; and thus increase the resolution of previously ambiguous phylogenetic relationships based on several cpDNA markers (Hu et al, 2016;Jansen et al, 2007). For example, Zeng et al (2017) used whole plastome sequences and coding genes to construct phylogenetic trees of Rehmannia, both of which indicated four nearly identical clades and had high levels of phylogenetic resolution. The noncoding regions in a plastome usually have higher variation rates than the coding genes (Hu et al, 2016;.…”