The first complete chloroplast genome sequence of Pentaphragma spicatum Merr. (Pentaphragmataceae) and phylogenetic analysis

Abstract

Pentaphragma spicatum Merr. is an endemic wild edible plant of China belonging to the Pentaphragmataceae family. It is widely consumed by Shangsi County resident in Guangxi Fangchenggang. Initially, Pentaphragma was classified as a genus within the Campanulaceae family, but, later it was treated as part of the Pentaphragmataceae family. However, the chloroplast genome of Pentaphragmataceae has not yet been reported. In this study, we sequenced the first complete chloroplast (cp) genome of P. spicatum from Guangxi, China. The whole genome was 154,229 bp in length, consisting of a pair of inverted repeats (IR each 25,572 bp), a large single-copy region (LSC 84,884 bp), and a small single-copy region (SSC 18,201 bp). The complete genome contained 129 genes, including 87 protein-coding genes, 34 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 37.71%. Based on a maximum-likelihood phylogenetic analysis, it has been determined that P. spicatum is not phylogenetically related to Campanulaceae and supports the decision to classify it as a separate family, Pentaphragmataceae. The complete chloroplast genome of P. spicatum will help enhance and integrate the existing genome data of Asterales. This will provide insights into the phylogenetic relationship within Campanulaceae.

Keywords: Complete chloroplast genome; pentaphragma spicatum merr; pentaphragmataceae; phylogenetic analysis.

Figure 1.

A. Plant image of Pentaphragma spicatum: Fleshy herb, short stem, with white or yellow-green corolla, and the sepals are shorter than the corolla. This photo was photographed by Sizhao Liu at Shangsi County in Guangxi. B. "voucher specimen of Pentaphragma spicatum.

Figure 2.

Schematic map of overall features of the P. spicatum chloroplast genome (genes drawn outside the outer circle are transcribed clockwise, and those inside are transcribed counter-clockwise. Genes belonging to different functional groups are color-coded. The different colored legends in the bottom left corner indicate genes with different functions. The dark grey inner circle indicates the GC content of the chloroplast genome and the presence of nodes in the LSC, SSC, IR regions).

Figure 3.

Consensus phylogenetic tree reconstructed by maximum likelihood (ML) and Bayesian inference (BI) analysis based on 56 protein-coding sequences (CDS) of 26 species, with Lithospermum erythrorhizon, Trigonotis peduncularis, and Cordia dichotoma as outgroups. Numbers near the branches are bootstrap support (BS) percentages obtained from maximum likelihood inference and posterior probabilities (PP) obtained from Bayesian analysis (BS/PP). those nodes with BS = 100%, PP = 1.00 were shown with asterisks. The following sequences were used: Cordia dichotoma NC_066967, adenophora stricta NC_036223 (Kyeong-Sik et al. 2017), aralia chinensis MZ351435, aster tataricus NC_042913 (Shen et al. 2018), calendula officinalis NC_066028, carpodetus serratus MF770619 (Knox 2014), centella asiatica MN854377, cichorium intybus NC_043842 (Yang et al. 2019), Codonopsis pilosula NC_060312, Cordia dichotoma NC_066967, Coriandrum sativum NC_029850, Eryngium foetidum NC_068234, Heptapleurum heptaphyllum NC_029764 (Zong et al. 2016), Hypochaeris radicata NC_044795, Ilex aquifolium NC_068798, Lithospermum erythrorhizon NC_053783, Lobelia chinensis NC_035370, Menyanthes trifoliata NC_041436, Nymphoides peltate NC_061690, Panax ginseng NC_006290, Pentaphragma spicatum OQ942205, Platycodon grandifloras NC_035642, Scaevola taccada NC_040933, Senecio scandens NC_073505, Stylidium petiolare MZ239204, Taraxacum mongolicum NC_031396, Trigonotis peduncularis NC_070037. The species newly sequenced in this study is shown in red font.