Abstract
This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family.
Highlights
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 [1,2,3]
The genome of C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia ranged from 156,560 bp (C. glandulosa) to 155,436 bp (M. oblongifolia); the coding region ranged from 78,080 bp (C. farinosa) to 76,614 bp Plants 2021, 10, 1229 (C. glandulosa), corresponding to 49.89% and 48.93% of the total genome length
The large single copy (LSC) regions ranged from 85,681 bp (C. glandulosa) to 84,153 bp (M. oblongifolia) in size, whereas the SSC ranged from 18,481 bp (M. oblongifolia) to 18,031 bp (C. glandulosa); the pair of inverted repeats are separated by the small single copy region and ranged from 26,430 bp (C. farinosa) to 26,294 bp (M. crassifolia) (Table 1 and Figure 1)
Summary
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 [1,2,3]. The four species in question are considered important medicinal plants and are used in the treatment of many diseases. Phylogenetic relationship studies using genes from chloroplast and nuclear genomes [29,33] confirmed the monophyly of Brassicaceae and Capparaceae. 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]. 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. We reconstructed the phylogenetic relationship between Capparaceae, Cleomaceae and Brassicaceae to infer the phylogenetic positions of the species within the families
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