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

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 to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced plastomes that represent all the three subgenera of , we detected (1) two independent relocations of the same five genes (-) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the gene in or the gene in both and ; (2) relocation of the gene from the LSC region to the inverted repeat (IR) region in ; (3) uniform inversion of an 11-14 kb segment (-) 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 (, , and 11 genes). In addition, we also found that the four 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 subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of .