Abstract: Owing to the advances of DNA sequencing technologies, at least 190 plastid genomes have been completely sequenced during the past two decades. Based on this unprecedented abundance of data, extensive genomic changes have been revealed in the plastid genomes. Inversion is the most common mechanism that leads to gene order changes. Several inversion events have been recognized as informative phylogenetic markers, such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all ferns. Gene loss is a common event throughout plastid genome evolution. Many genes were independently lost or transferred to the nuclear genome in multiple plant lineages. The trnR-CCG gene was lost in some clades of lycophytes, ferns and seed plants, and all the ndh genes were absent in parasitic plants, gnetophytes, Pinaceae and the Taiwan moth orchid. Certain parasitic plants have particularly lost plastid genes related to photosynthesis because of the relaxation of functional constraint. The dramatic growth of plastid genome sequences has also promoted the utilization of whole plastid sequences and genomic features to solve phylogenetic problems. Chloroplast phylogenomics has provided additional evidences for deep-level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic levels. However, chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed.

Key words: plastid genome sequencing, comparative genomics, chloroplast phylogenomics, genome rearrangement, gene loss.