AUTHOR=Xu Xiaodong , Wang Dong 

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

JOURNAL=Frontiers in Plant Science

VOLUME=11

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.600354

DOI=10.3389/fpls.2020.600354

ISSN=1664-462X

ABSTRACT=<p>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 <italic>Corydalis</italic> to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced <italic>Corydalis</italic> plastomes that represent all the three subgenera of <italic>Corydalis</italic>, we detected (1) two independent relocations of the same five genes (<italic>trnV-UAC</italic>-<italic>rbcL</italic>) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the <italic>atpH</italic> gene in <italic>Corydalis saxicola</italic> or the <italic>trnK-UUU</italic> gene in both <italic>Corydalis davidii</italic> and <italic>Corydalis hsiaowutaishanensis</italic>; (2) relocation of the <italic>rps16</italic> gene from the LSC region to the inverted repeat (IR) region in <italic>Corydalis adunca</italic>; (3) uniform inversion of an 11–14 kb segment (<italic>ndhB</italic>-<italic>trnR-ACG</italic>) in the IR region of all the four Corydalis species (the same below); (4) expansions (&gt;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 (<italic>accD</italic>, <italic>clpP</italic>, and 11 <italic>ndh</italic> genes). In addition, we also found that the four <italic>Corydalis</italic> 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 <italic>Corydalis</italic> subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of <italic>Corydalis</italic>.</p>