Plastome structure, evolution and diversity of Frankincense-producing Boswellia genus

The genus Boswellia is famous for its commercially important frankincense production. Additionally, it has unique ecological and taxonomic importance. However, the Boswellia species often face natural hybridization, and the lack of genomic datasets frequently contributes to taxonomic uncertainties. Here, we sequenced and analyzed the complete plastid genomes (plastomes) of six Boswellia species (B. carteri, B. bullata, B. dioscoridis, B. elongata, B. serrata, B. frereana, and a hybrid variant of B. sacra (B. sacra var. supersacra). The genome size of Boswellia plastomes is between 159,189 bp and 160,743 bp, displaying a typical structure with large single-copy (LSC; 86,811–88,054), small single-copy (SSC; 26,666–26,763), and inverted repeat (IR; 26,544–26,763) regions. The IR regions (~ 25,000 bp) are highly conserved across species, contributing to the stability of the plastome structure. Our study identified consistent gene content, typical of angiosperms, and showed that the IR boundaries remained unchanged across species. The simple sequence repeats revealed a range between 43 and 52 across the plastomes, with B. sacra exhibiting the highest count. We detected long, repetitive sequences that could serve as useful genetic markers for species differentiation. Nucleotide diversity analysis highlighted significant gene variations (matK, rbcL, rpl14, and rpoC2). The results showed substantial genetic divergence in regions (rpl14, matK, and rpoC2), demonstrating distinct variations among species. In evolutionary history, the B. carteri diverged around 4.2 million years ago (mya), while B. sacra and B. serrata separated by approximately 7.0 mya. The phylogenomic analysis supported the distinction between B. carteri and B. sacra, challenging prior claims that these are synonymous. These findings contribute to a deeper understanding of species boundaries within Boswellia and offer valuable resources for future DNA barcoding efforts.