Revealing the Dynamic History of Parasitic Plant Plastomes via Structural Characterization, Comparative Analysis, and Phylogenomics

Background: The shift to a parasitic lifestyle in plants often leaves distinct marks on their plastid genomes, given the central role plastids play in photosynthesis. Studying these unique adaptations in parasitic plants is essential for understanding the mechanisms and evolutionary patterns driving plastome reduction in angiosperms. By exploring these changes, we can gain deeper insights into how parasitism reshapes the genomic architecture of plants. Method: This study analyzed and compared the plastomes of 113 parasitic plants from different families. Results: The Orobanchaceae family (hemiparasitic plants) displayed the largest plastome size, while Apodanthaceae exhibited the shortest. Additionally, Orobanchaceae showcased little to no gene loss in their plastomes. However, holoparasitic species typically had reduced plastome sizes. Convolvulaceae exhibited significantly reduced plastome sizes due to high gene loss, and Apodanthaceae retained only a few genes. Gene divergence among different families was also investigated, and rps15, rps18, and rpl33 in Orobanchaceae; accD and ycf1 in Convolvulaceae; atpF and ccsA in Loranthaceae; and rpl32 in Santalaceae showed greater divergence. Additionally, Orobanchaceae had the highest numbers of all repeat types, whereas Loranthaceae and Convolvulaceae exhibited the lowest repeat numbers. Similarly, more simple sequence repeats were reported in Loranthaceae and Santalaceae. Our phylogenetic analysis also uncovered a distinct clade comprising Loranthaceae, with a single Schoepfiaceae species clustering nearby. Contrary to expectations, parasitic and hemiparasitic plants formed mixed groupings instead of segregating into separate clades. Conclusions: These findings offer insights into parasitic plants’ evolutionary relationships, revealing shared and divergent genomic features across diverse lineages.