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Boswellia sacra  (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of  B .  sacra . The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions.  De novo  assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the  B .  sacra  cp genome is closely related to the cp genome of  Azadirachta indica  and  Citrus sinensis , while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of  B .  sacra  and  A .  indica  was highest for  atpA ,  rpl2 ,  rps12  and  ycf1 . The cp genome of  B .  sacra  reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman