Plastome evolution in Aurantioideae and plastome-based classification of Citrus

Plastomes are widely used in plant systematics and also retain signals of structural evolution. In this study, we investigated plastome evolution in the subfamily Aurantioideae of Rutaceae, focusing on structural variation at the LSC–IR boundary regions, putative pseudogenization of plastid genes, plastome-based classification of Citrus , and divergence-time patterns. Comparative analyses revealed substantial structural variation around the rpl22 and rps19 regions at the LSC–IR boundaries and repeated pseudogenization of plastid genes such as rpl22 , ycf68 , and orf56 . Additional lineage-specific sequence disruptions were detected in cemA , ycf15 , rps4 , and ycf1 . Phylogenetic analyses of complete plastomes from 56 Citrus accessions resolved eight major plastome clusters within Citrus . Divergence-time analysis indicated two comparable Asia–Africa splits within Aurantioideae, whereas the divergence between Australian and Asian Citrus lineages was more recent. These results show that plastome evolution in Aurantioideae combines phylogenetically informative sequence variation with recurrent local structural change and provides useful information for classification and evolutionary interpretation in this economically important plant group.