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The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed  Corydalis  to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced  Corydalis  plastomes that represent all the three subgenera of  Corydalis , we detected (1) two independent relocations of the same five genes ( trnV-UAC - rbcL ) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the  atpH  gene in  Corydalis saxicola  or the  trnK-UUU  gene in both  Corydalis davidii  and  Corydalis hsiaowutaishanensis ; (2) relocation of the  rps16  gene from the LSC region to the inverted repeat (IR) region in  Corydalis adunca ; (3) uniform inversion of an 11–14 kb segment ( ndhB - trnR-ACG ) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes ( accD ,  clpP , and 11  ndh  genes). In addition, we also found that the four  Corydalis  plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three  Corydalis  subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of  Corydalis .

Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements