Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

• Published in: Scientific reports 2022-08, Vol.12 (1), p.14241-14241, Article 14241
• Main Authors: Yin, Xianmei, Huang, Feng, Liu, Xiaofen, Guo, Jiachen, Cui, Ning, Liang, Conglian, Lian, Yan, Deng, Jingjing, Wu, Hao, Yin, Hongxiang, Jiang, Guihua
• Format: Article
• Language: English
• Subjects: 631/181/757; 631/208/726; Chloroplasts; Corydalis; Endemic species; Genetic transformation; Genomes; Humanities and Social Sciences; Inverted repeat; multidisciplinary; Phylogenetics; Phylogeny; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-17721-y

Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata , C. mucronate , and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes ( trnM-CAU-rbcL ) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11–14-kb segment ( ndhB-trnR-ACG ) was found in the inverted repeat region; and extensive losses of accD , clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis . In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.