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Background   Salvadora persica  L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of  S. persica  for the first time and compared it with 11 related specie’s cp genomes from the order Brassicales.    Results  The  S. persica  cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in  M. oleifera,  while in  S. persica  it was the smallest (153,379 bp). The cp genome of  S. persica  encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides,  S. persica  contains 27 forward, 36 tandem and 19 palindromic repeats. The  S. persica  cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between  S. persica  and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that  S. persica  formed a single clade with  A. tetracantha  with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea.    Conclusion  The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of  S. persica  in complex angiosperm families.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07626-x.

bmc genomics

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales