Complete chloroplast genomes of 19 species of Pedicularis (Orobanchaceae): comparative genome and phylogenetic analysis

The genus Pedicularis is a large genus of Orobanchaceae including many species used as ethnic or folk medicine. However, its genome data is still poor. We reported the chloroplast (cp) genome of 19 species of Pedicularis for the first time. They were 144,279–162,362 bp in length and displayed a typical quadripartite structure. A total of 117–133 genes were annotated and the loss of the ndh gene was discovered to vary among different species. The cp DNA sequences mostly ended in Adenine (A) or Uracil (U). We detected no genome rearrangement in 19 cp genomes but observed the expansion of IR regions in P. oliveriana. We discovered 35–62 simple sequence repeats (SSRs) and 38–88 long terminal repeats (LTRs). Nucleotide diversity analysis showed that five variable regions may have contributed to the identification of the genus. Ka/Ks values indicated that purifying selection was probably the major force in the evolution of Pedicularis. Phylogenetic analysis showed that the 19 species of Pedicularis were clustered into two main clades. One was formed by alternated leaves groups and the other clades were formed by opposite or whorled leaves groups. Therefore, phyllotaxy may reflect the infra-genetic relationship of species in Pedicularis. Furthermore, our study supports that alternated leaves were primitive characters for the genus Pedicularis.