*3.4. Sequence Analysis*

MEGA 6.0 was used to compute the codon usage, base composition, and the relative synonymous codon usage values (RSCUs). The RNA editing sites in cp protein-coding genes of the Capparaceae species were predicted using PREP suite [76] with a 0.8 cutoff value. Simple sequence repeats (SSRs) were identified in the chloroplast genomes of the four species (*C. farinosa, C. glandulosa, M. crassifolia* and *M. oblongifolia*) using the online software MIcroSAtellite (MISA) [77] with the following parameters set: eight, five, four and three repeat units for mononucleotides, dinucleotides, trinucleotides and tetra-, penta-, hexanucleotide SSR motifs, respectively. To identify the size and location of long repeats (palindromic, forward, reverse and complement) in the four species of Capparaceae being studied, the online program REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputer (accessed on 22 June 2019) [76], with standard settings, was used.
