**1. Introduction**

The family Capparaceae, whose members are distributed in both arid and semi-arid areas, has about 470 morphologically diverse species in ca. 17 genera, which include *Cadaba* and *Maerua* [1–3]. Members of the family possess highly essential compounds used in folk medicine that are extracted from them [4]. The four species in question are considered important medicinal plants and are used in the treatment of many diseases. Most *Cadaba* species contain important compounds, such as alkaloids, sesquiterpene lactones and cadabicine. *Cadaba farinosa* and *Cadaba glandulosa* are used as purgative, anthelmintic, antisyphilitic, emmenagogue, aperient, antiscorbutic, and antiphlogistic substances; for liver damage and cancer, dysentery, fever and body pain; in therapy as a hepatoprotective and hypoglycemic [5,6]. *Maerua crassifolia* and *Maerua oblongifolia* species are used in the treatment of fever, stomach troubles, skin infections, diabetes mellitus, epilepsy and abdominal colic; they demonstrate antimicrobial and antioxidant properties and are used

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**Citation:** Alzahrani, D.A.; Albokhari, E.J.; Yaradua, S.S.; Abba, A. Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution. *Plants* **2021**, *10*, 1229. https://doi.org/10.3390/ plants10061229

Academic Editors: Nunzia Scotti and Rachele Tamburino

Received: 4 March 2021 Accepted: 31 May 2021 Published: 17 June 2021

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**Copyright:** © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

for hypocholesterolemia, wound-healing, intestinal disorders like abdominal cramps and hookworms, anthrax, severe mumps, tetanus and eye disease [5,7–11].

According to the taxonomic status of Capparaceae, Capparideae was placed under the cohort Parietales [12]. Later, Capparidaceae and Cruciferae were placed under suborder Capparidineae, order Rhoedales [13], and Capparidaceae was classified under Capparidales [14,15]. After some decades, Capparaceae was placed under Capparales [1,16], and finally under order Brassicales [17–20]. Previous studies, with the exception of Hutchinson [14], reported that Brassicaceae and Capparaceae are sister taxa [1,21–30]. The two families (Brassicaceae and Capparaceae) are considered as one family—Brassicaceae sensu lato (s.l.)—by some authors [17,18,31,32]. Phylogenetic relationship studies using genes from chloroplast and nuclear genomes [29,33] confirmed the monophyly of Brassicaceae and Capparaceae. Within Capparaceae, there are two subfamilies, Cleomoideae and Capparoideae; these subfamilies are elevated to family by some studies of Brassicales [14,34]. Currently, as adopted by the Angiosperm Phylogeny Group [19,20], Cleomaceae, Capparaceae and Brassicaceae are considered as a single family.

There has been some shifting of a few genera between the families Brassicaceae and Capparaceae, such as two genera, *Dipterygium* and *Puccionia*, previously belonging to Brassicaceae [14] being moved to Capparaceae under the subfamily Dipterigioideae, based on the presence of methyl-glucosinolate [35,36]. The genus *Stixis* L. was removed from the Capparaceae family and represents as a new family, which is called Stixaceae Doweld (including the genus *Forchhammeria* Lieb.), yet, it is still considered under Brassicaceae sensu lato, excluding *Forchhammeria,* as it is more closely related to Resedaceae than Brassicaceae [37].

Genetic information is a reliable means of understanding evolutionary relationships among species in various taxonomic hierarchies. The genetic information in the chloroplast genome contains sufficient information for comparison analysis and studies of species diversification, due to the presence of functional genes that have a vital role in plant cells [38]. The chloroplast organelle functions in carbon fixation and photosynthesis in plants [39]. The chloroplast genome is more conserved than other genomes found in plants. Generally, the chloroplast genome is circular, double-stranded and has a quadripartite structure, including a large single copy (LSC), as well as a small single copy (SSC) and a pair of repeats (IRa and IRb) [40]. The chloroplast genome is uniparentally inherited, and this characteristic makes it highly conserved in structure and gene content [41,42]. However, different kinds of mutations do occur [43], which consequently lead to sequence divergence among species and could be used to study evolutionary relationships in plants [44]. Despite the importance of the plastome in modern taxonomy, chloroplast genomes of only three species in the whole Capparaceae family, including three varieties, have been reported: *Capparis spinosa* [45], *Capparis spinosa* var. *spinosa*, *Capparis spinosa* var. *herbacea*, *Capparis spinosa* var. *ovata* [46] and *Capparis decidua*.

This study obtained the first complete chloroplast genome of the genus *Cadaba* (*Cadaba farinosa* and *Cadaba glandulosa*) and genus *Maerua* (*Maerua crassifolia* and *Maerua oblongifolia*) using Illumina sequencing technology. This study also analyzed and compared the features of the cp genomes to provide resources of genetic data for the four species. We reconstructed the phylogenetic relationship between Capparaceae, Cleomaceae and Brassicaceae to infer the phylogenetic positions of the species within the families.

## **2. Results**
