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 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.

Characterization of the complete chloroplast genome of Corydalis bungeana Turcz

“…The results suggested that C. bungeana was separated from other species of Corydalis though it was classified into the genus of Corydalis yet and the previous study with DNA barcoding also demonstrated that C. bungeana was classified into a single clade in phylogenetic tree of Corydalis based on ITS and matK (Ren et al 2019). This evolutionary analysis also provided the evidence for Corydaleae had a close relationship with Lamprocapnos spectabilis from the Fumarioideae (Papaveraceae) clade (Lid en et al 1997;Xu and Wang 2021).…”

“…This evolutionary analysis also provided the evidence for Corydaleae had a close relationship with Lamprocapnos spectabilis from the Fumarioideae (Papaveraceae) clade (Lidén et al. 1997 ; Xu and Wang 2021 ).…”

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

“…Non-synonymous/Synonymous mutation ratio (Ka/Ks) is comprehensively effective in the detection of selection pressures in proteins or fragments of DNA sequences in plant species ( Wang et al, 2010 ; Gao L. Z. et al, 2019 ; Xu and Wang, 2021 ). It is key in analyzing the evolutionary pressures within the genome.…”

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

“…Within Euphorbia , the length of LSC, IRs, SSC, and whole plastome are highly variable, with some 42 kb variation ranging from the shortest ( c. 136 kb) to the longest ( c. 178 kb; Table 1 ; Figure 1 ). Several factors that contribute to the variation in plastome sizes include gene inversions and duplications, losses/pseudogenizations, and IR expansions/contractions ( Xu and Wang, 2021 ). In particular, the expansions of the IR into the SC (LSC/SSC) regions have contributed the most to the increase of plastome size in E. tithymaloides and E. schlechtendalii .…”

“…Then, tandem repeats were detected using the Tandem Repeats Finder v.4.0.9 ( Benson, 1999 ). Following the protocol of Xu and Wang (2021) , the maximum period size, minimum alignment score to report repeat, maximum TR array size (bp, millions), alignment parameters of match, mismatch, indels, were set to 500, 80, two, two, seven, and seven, respectively. Lastly, REPuter ( Kurtz et al, 2001 ) was used to identify four types of dispersed repeat elements (Forward, Reverse, Complement, and Palindromic) based on the criteria: minimum repeat size equal to 30 bp, and Hamming distance equal to three, following the setting by Cauz-Santos et al (2020) .…”