Plastome comparison and phylogenomic analysis of threatened wild Egyptian Capparis taxa

Capparis is one of the largest genera in the Capparaceae family, it is currently classified as comprising threatened wild plants in Egypt. The taxonomy of Capparis remains ambiguous due to complex classifications, overlapping morphological traits, and regional variability. Herein, we present, for the first time, the complete plastome genome sequences of five threatened Capparis taxa from Egypt, all belonging to Capparis spinosa, including one subspecies and several varieties. Together with 13 additional plastomes in the Capparaceae family from public databases, we conducted detailed structural and phylogenetic analyses to explore taxonomic relationships and enhance the molecular understanding of this complex genus.

The results revealed significant variations in tetrad structure among the Egyptian taxa, particularly at the IR/LSC/SSC junctions, as well as unique gene rearrangements. SSR repeats and codon usage bias may also contribute to shaping plastome diversity. Both mutational forces and natural selection contributed to genome size variation at low taxonomic levels. Phylogenomic analysis strongly supported the taxonomic relationships among Egyptian Capparis taxa and their relatives, shedding light on evolutionary divergence within the genus. Divergence time estimates suggested that the crown node age of Capparaceae originated in the mid-Miocene, approximately 18.62 million years ago (Mya), while the divergence of Egyptian Capparis genotypes occurred around 1.7 Mya during the Pleistocene. Capparis spinosa var. deserti and Capparis spinosa var. herbacea exhibited highly similar plastome organization structures, supporting a close evolutionary relationship between these two wild varieties.

This comparative plastome genome approach served as an effective tool for studying plant lineage evolution, taxonomy, and developing genetic markers for accurate identification of Capparis taxa and the evolution of the Capparaceae family.