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Background  The plastome of medicinal and endangered species in Kingdom of Saudi Arabia,  Barleria prionitis  was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships.    Results  The plastome of  B. prionitis  was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes,  ycf1 and  ndhF  and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection ( atpF, petD, psbZ, rpl20, petB, rpl16 ,  rps16, rpoC, rps7, rpl32  and  ycf3 ). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition,  Barleria ,  Justicia  and  Ruellia  are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes.    Conclusions  This study sequenced and assembled the first plastome of the taxon  Barleria  and reported the basics resources for evolutionary studies of  B. prionitis  and tools for phylogenetic relationship studies within the core Acanthaceae.

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae