Nineteen complete chloroplast genomes of the genus Pedicularis in Tibet: Comparative genome and phylogenetic analysis

The genus Pedicularis has a large number of members and large interspecific variation morphologically. Traditional taxonomy placed too much emphasis on the weight of morphological traits in the taxonomy of the genus, which has led to the long-standing controversy over the phylogenetic relationship. In this study, 19 chloroplast(cp) genomes of Pedicularis species were sequenced, assembled, characterized and conducted phylogenetic analysis for the first time. The results showed that the 19 cp genomes were 144,279-162,362 bp in length, comprising 117-133 genes, and ndh family were lossed commonly in those genomes. The codons usage perference of those genomes ended in A/T. Forward (F) Palindromic (P) were dominant in the long terminal repeats (LTRs) and A/T was dominant in the simple sequence repeats (SSRs). According to IRb/SSC, the 19 genomes could be classified into four types. Seven hotspots were identified in the LSC and SSC regions. The Ka/Ks ratio showed ndhB、ndhG、ndhE、ndhA and ndhC were strongly purified. Phylogenetic trees showed the genus Pedicularis belonged to Orobanchaceae and was closely related to Cistanche and Castilleja, but it was not a monophyletic group; In addition, the results did not fully support the taxonomy of the genus Pedicularis into 13 grexs but were consistent with the taxonomy obtained based on phyllotaxy. Therefore, cp genome and phyllotaxy may could be the main criteria for the taxonomy of the genus. This study provides a scientific basis for the identification, taxonomy, phylogeny and molecular biology research of the genus Pedicularis.