Plastome insights from the mistletoe Dendrophthoe pentandra (Loranthaceae) highlight gradual evolutionary footprints of parasitism in Santalales.

Our newly assembled plastomes of Dendrophthoe pentandra, a widespread mistletoe from Indonesia, reveal extensive gene loss, refined annotation, and evolutionary patterns that highlight the gradual degradation of plastomes in hemiparasites within Santalales. Mistletoes, long valued for their ecological and medicinal importance, reveal a hallmark of parasitism: chloroplast genome (plastome) reduction. Despite being the most widespread mistletoe in Indonesia, Dendrophthoe pentandra was previously represented by only two plastomes from China, limiting broader evolutionary interpretation. We report two plastomes from Indonesia and analyze them within a comparative framework spanning parasitic and non-parasitic relatives across Santalales. Both plastomes (122,298 bp and 122,291 bp) exhibited extensive gene loss, including most photosynthesis-related ndh genes as well as rpl32, rpl36, rps15, rps16, and trnK-UUU. Pseudogenization affected trnA-UGC, ycf15, ycf1, rpl2, infA, and ndhB. High-depth mapping against multiple plastome references confirmed that these features reflect genuine parasitic reduction rather than artifacts of limited sequencing depth. Our plastomes were slightly longer and had more complete gene annotations than those previously reported accessions. Despite several tRNA gene losses, amino acid frequencies and codon usage remained conserved. Additionally, 103-105 simple sequence repeats and 35-38 tandem repeats were identified as potential molecular markers. Phylogenomic analyses positioned D. pentandra within mistletoe lineages of Santalales, clearly separated from euphytoids and non-parasitic relatives. Comparative analyses revealed that plastome size reduction correlated with parasitism intensity. Gene loss, pseudogenization, and variable inverted repeat junctions further highlighted the genomic footprints of parasitism. Fine-scale alignments with close relatives showed no evidence of extreme rearrangements. Collectively, our findings support a gradual trajectory of plastome degradation in Santalales-from complete plastomes in non-parasitic species, to moderate reduction in euphytoids, and extensive loss in mistletoes-underscoring key genomic adaptations to parasitism.