Comparative analysis of chloroplast genomes in <i>Commiphora gileadensis</i> from Saudi Arabia and Oman reveal evolutionary genetic divergence

This study aimed to elucidate chloroplast structure of the wild plant Commiphora gileadensis growing in Saudi Arabia and to compare it with that of the same species grown in Oman. The the two versions exhibited distinct cycles of contraction and expansion, particularly in the small single copy and inverted repeat regions. These variations are attributed to ∼1200 genetic changes, including SNPs and Indels, predominantly occurring in the genic region. Of these mutations, 165 are transitions and 535 are transversions. Nine frameshift mutations were identified in genes encoding DNA-dependent RNA polymerase (e.g. rpoC2 and rpoC1), protease (e.g. clpP), and NADH dehydrogenase (e.g. ndhD and ndhA). Mutations in these crucial genes suggest the potential occurrence of heteroplasmy in the chloroplasts from the two origins. Several essential genes were uniquely present in the Saudi chloroplast, while others were unique to the Omani chloroplast. These chloroplast genes are involved in self-replication and photosynthesis. We hypothesize that the genetic divergence between the two chloroplastsresults from exposure to evolutionary forces. These genetic differences are compensatory, as some genes may complement the functions of the missing ones. Elucidating the genomic architecture of chloroplasts provides insights into the interplay of ecological determinants that shape the phylogenetic affinities among plant taxa.