Abstract
Chloroplast genomes (plastomes) have long been considered structurally conserved, but recent sequencing efforts have uncovered pervasive rearrangements that challenge this assumption. This review catalogues the main types of plastome modifications: large and small inversions; insertions and deletions (indels); gene and intron losses; horizontal gene transfers; shifts in inverted repeat boundaries; and gene duplications. It then explains the molecular processes that generate these changes, from repeat-mediated recombination and slipped-strand mispairing to rare foreign-DNA integration events. These structural variants serve as informative phylogenetic markers, enabling resolution of both ancient divergences and recent radiations within angiosperms. Beyond their value for systematics, plastome rearrangements can reshape gene order and copy number, with measurable effects on gene expression, metabolic pathways, and photosynthetic efficiency. Evidence shows that, in certain lineages, plastid genes have been transferred to the nucleus to compensate for gene loss and preserve essential cellular functions. Looking ahead, three emerging approaches promise to deepen our understanding of plastome dynamics: comprehensive pan-plastome surveys coupled with long-read sequencing of under-sampled lineages; targeted plastid transformation to engineer specific rearrangements; and advanced genome editing to test their adaptive significance. Together, these strategies will illuminate how plastid structural change impacts plant evolution and adaptation.