The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

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Blepharis ciliaris is an important medicinal plant and endemic species in Saudi Arabia. This study reported the complete chloroplast genome of B. ciliaris, the second to be sequence in non cystolith clade of Acanthaceae. The genome is 149, 717 bp in size and consisted of a pair of inverted repeat (25, 331 bp each) separating the two single copy region, the large single copy (LSC) 82, 057 bp and small single copy SSC 16, 998 bp. The plastome has overall GC content of 38.5% and 112 genes comprising of 79 protein coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic relationship analysis showed that B. ciliaris is sister to Aphelandra knappiea. The cp genome reported in this study will useful in genetic diversity and evolutionary studies of the species.