The complete chloroplast genome of the medicinally important plant Plumbago zeylanica L. (plumbaginaceae) and phylogenetic analysis

Abstract Plumbago zeylanica L. 1753 is a medicinally-important herb in family Plumbaginaceae. In this study, we assembled and reported the complete chloroplast genome of P. zeylanica. The plastome of P. zeylanica was 169,178 bp, including a large single-copy region of 92,135 bp, a small single-copy region (SSC) of 13,455 bp and a pair of inverted repeat regions (IRs) of 31,794 bp. It contained 124 genes, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that P. zeylanica formed a close relationship with P. auriculata in Plumbago. The first complete chloroplast genome report of P. zeylanica providing an opportunity to explore the genetic diversity, and would be also helpful in the species identification and conservation.


Introduction
Plumbago species are mainly distributed in warm tropical regions of the world.Three species within the genus, including Plumbago indica L. 1754, Plumbago zeylanica L. 1753 and Plumbago auriculata Lam.1786, are important medicinal plants and are widely cultivated around the world (Sandeep et al. 2011;Koutroumpa et al. 2018).P. zeylanica, commonly known as white chitrak, is a perennial herbs or shrubs in Plumbaginaceae (Figure 1).It is supposed to be originated in South-East Asia and is one of the medicinal plants used in the Indian and China traditional system of medicine (Sheeja et al. 2010).Plumbagin is a highly potent and broad-spectrum biological compound, and it is mainly extracted from the root and leaves of P. zeylanica (Yuvaraj and Jalalpure 2011;Adusei et al. 2019;Choudhary et al. 2021).Plumbagin displays various potential medicinal properties such as anticancer, anti-fungal, anti-inflammatory, anti-bacterial, anti-fertility, anti-malarial and Antidiabetic (Sheeja et al. 2010;Choudhary et al. 2021).
Plumbago zeylanica is the most commonly cultivated and utilized species in Plumbago for its medicinal and pharmacological properties (Checker et al. 2009;Shukla et al. 2021).However, the complete chloroplast genome sequence of P. zeylanica has not been reported.At present, the phylogeny  of Plumbago is still not clear due to the incomplete sampling and fragment markers providing insufficient informative loci (Koutroumpa et al. 2018).We expect the complete chloroplast genome sequence of P. zeylanica will benefit the phylogenetic analysis of Plumbago and Plumbaginaceae and believed that it will helps to explore the genetic diversity and population structure of P. zeylanica.

Results
The short reads coverage depths of the assembled genome can be seen in Figure S1.The length of the complete chloroplast genome sequence of P. zeylanica was 169178 bp, with a large single copy (LSC) region of 92135 bp, a small single copy (SSC) region of 13455 bp. and two separated inverted repeated (IR) regions of 31749 bp (Figure 2).A total of 124 genes were identified in the chloroplast genome of P. zeylanica, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes.Thirteen genes are cis-splicing genes which contain introns (Figure S2), rps12 is a trans-splicing gene (Figure S3).In IR regions, 18 genes were detected, including ycf1, rrn5,rrn4.5,rrn23,rrn16,rps7,ndhB,ycf2,rpl32,rpl2,rps19.The overall GC content was 37.2%, and the corresponding contents for LSC, SSC and IR regions were 35.1%, 31.7% and 41.3%, respectively.We detected 84 SSR markers ranging from mononucleotide to trinucleotide repeat motif.The Phylogenetic results demonstrated a close relationship between P. zeylanica and P. auriculata in the Plumbago clade (Figure 3).The complete plastome sequence of P. zeylanica will not only provide effective use of this species, but also for the phylogenetic studies of Plumbaginaceae.

Discussion and conclusion
In this study, we sequenced and assembled the complete chloroplast sequence of P. zeylanica.We also elucidated all the genes in the complete chloroplast genome of species.Plumbago comprise medicinally important species around the world, the first complete chloroplast genome report of P. zeylanica providing an opportunity for further research on the species and Plumbago.This powerfully molecular genetic markers can be used to explore the genetic diversity, and would be also helpful in the species identification and conservation in genetic level.Phylogenetic analysis revealed a sister relationship between P. zeylanica and P. auriculata.The chloroplast genomes of the two species displayed similar gene content and gene order.Plumbago species are mainly distributed in warm tropical regions with approximately 20 species (Sandeep et al. 2011;Koutroumpa et al. 2018).In this genus, only one species' chloroplast genome has been reported in previous research (Yao et al. 2019).To have a better understanding the relationships between species and detect the chloroplast genome structures features in Plumbago, we should conduct more extensive sampling.More species' chloroplast genomes need to be sequenced and assembled in the future research.

Figure 2 .
Figure 2. Circular map of the P. zeylanica chloroplast genome.Genes shown inside the circle are transcribed clockwise, those outside the circle are counterclockwise transcribed.The light grey and the darker grey in the inner circle represent at and GC content, respectively.Different functional groups of genes are signed according to the colored boxes.LSC: large single copy; SSC: small single copy; IRA/IRB: Inverted repeat regions.
CONTACT Huajie Zhang zhanghuajie@wbgcas.cnCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2333574.