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 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.
Highlights
The chloroplast genome of angiosperms is generally highly conserved in terms of structural organization, gene content, and gene arrangement (Palmer, 1985; Wicke et al, 2011; Ruhlman and Jansen, 2014; Mower and Vickrey, 2018)
The four newly sequenced complete plastomes ranged in length from 165,416 to 196,128 bp (Table 2)
We found that the inverted repeat (IR) of the Corydalis plastomes expanded markedly at the IR/small single-copy (SSC) boundaries (Figures 3, 4), which has resulted in the second to seventh largest IR sizes and the three smallest and sixth to eighth smallest SSC sizes in Ranunculales
Summary
The chloroplast genome (plastome) of angiosperms ( photosynthetic members) is generally highly conserved in terms of structural organization, gene content, and gene arrangement (Palmer, 1985; Wicke et al, 2011; Ruhlman and Jansen, 2014; Mower and Vickrey, 2018). Plastome rearrangements, if they occurred, tend to be relatively minor. Corydalis may represent an appropriate group to explore how the plastome content and structure have varied in a fine scale in the evolution history, when the unusual plastome rearrangements have originated, and why those changes have happened. A robust backbone phylogeny of this genus, which is instructive for taxonomy and systematics, is still not completed due to the lack of enough genetic resources
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