Supplementary files for “Comparative plastid genomics of Elaeagnaceae: Resolving phylogeny and revealing structural evolution”

Despite having an established backbone phylogeny of Elaeagnaceae, the intrageneric relationships within Elaeagnus remain elusive, and family-wide plastome evolution is poorly explored. We analyzed 71 plastomes of 62 species, including four newly sequenced Elaeagnus L. samples, to reconstruct phylogenies using protein-coding genes (PCGs), intergenic spacers (IGS), and complete sequences. Among these datasets, PCGs provided the strongest resolution, clarifying interspecific and infraspecific relationships within Hippophae L. However, Elaeagnus topologies remained poorly resolved across all datasets, suggesting a history of rapid evolutionary radiation. Plastome structure was highly conserved in Elaeagnaceae, except for lineage-specific IR expansion in Hippophae. Additionally, we identified repeat sequences and signals of positive selection. This study provides essential plastomic resources for understanding the phylogenetic complexity and adaptive evolution of Elaeagnaceae.