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

Abstract

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 <i>Corydalis</i> to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced <i>Corydalis</i> plastomes that represent all the three subgenera of <i>Corydalis</i>, we detected (1) two independent relocations of the same five genes (<i>trnV-UAC</i>-<i>rbcL</i>) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the <i>atpH</i> gene in <i>Corydalis saxicola</i> or the <i>trnK-UUU</i> gene in both <i>Corydalis davidii</i> and <i>Corydalis hsiaowutaishanensis</i>; (2) relocation of the <i>rps16</i> gene from the LSC region to the inverted repeat (IR) region in <i>Corydalis adunca</i>; (3) uniform inversion of an 11-14 kb segment (<i>ndhB</i>-<i>trnR-ACG</i>) 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 (<i>accD</i>, <i>clpP</i>, and 11 <i>ndh</i> genes). In addition, we also found that the four <i>Corydalis</i> 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 <i>Corydalis</i> subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of <i>Corydalis</i>.