Characterization of the Chloroplast Genome Structure of Gueldenstaedtia verna (Papilionoideae) and Comparative Analyses among IRLC Species

The genus Gueldenstaedtia belongs to Papilionaceae’s inverted repeat-lacking clade (IRLC) and includes four species distributed throughout Asia. We sequenced the chloroplast genome of G. verna and compared it with those of the IRLC clade. The genome was 122,569 bp long, containing 77 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analyses showed that G. verna lost one inverted repeat region, the rps16 gene, an intron of rpoC1, and two introns of clpP. Additionally, G. verna had four inversions (~50 kb inversion, trnK–psbK; ~28 kb inversion, accD–rpl23; ~10 kb inversion, rps15–trnL; ~6 kb inversion, trnL–trnI) and one reposition (ycf1). Its G + C content was higher than that of other IRLC species. The total length and number of repeats of G. verna were not significantly different from those of the other IRLC species. Phylogenetic analyses showed that G. verna was closely related to Tibetia. A comparison of substitution rates showed that ycf2 and rps7 were higher than one, suggesting that these were positive selection genes, while others were related to purified selection. This study reports the structure of the chloroplast genome of a different type, i.e., with four inversions and one reposition, and would be helpful for future research on the evolution of the genome structure of the IRLC.