Figure 1. Circular maps of Cymbaria chloroplast genomes.
The chloroplast genome sequences of C. mongolica and C. daurica contained 105 and 100 intact genes, respectively (Fig. 1; Table S1). Cymbaria contained 26 tRNA and four rRNA genes, while the number of PCGs and pseudogenes varied between two species. In contrast to the autotrophic Lindenbergia philippensis , C. mongolicaencoded 75 PCGs, and one pseudogene and lacked seven genes whileC. daurica encoded 70 PCGs, and three pseudogenes and lacked ten genes. Among the 15 intron-containing genes, 12 genes contained one intron, and the remaining three genes harbored two introns (Table S1). In addition, purifying or neutral selection was detected on all PCGs, with the exception of ycf 2, which was under positive selection. No pronounced differences were detected in the boundary regions. An inversion of large gene blocks (rbc L-mat K) was identified in the LSC region according to the Mauve alignment (Fig. S2). Four pairs of palindromic repeats (123, 67, 48, and 37 bp) and three pairs of palindromic repeats (190, 152, and 121 bp) were detected at both ends of the inverted region of C. mongolica (54,654 bp size) and C. daurica (55,904 bp size), respectively.
We estimated the sequence divergence and gene content for 54 chloroplast genomes within the family Orobanchaceae (Fig. 2; Table S2). The genome sizes of the autotrophs (153,622–155,319 kb, mean: 154,213 kb) and hemiparasites (142,733–160,910 kb, mean: 151,152 kb) were similar; however, the genome sizes of the autotrophs were higher than those of the holoparasites (45,673–150,504 kb, mean: 87,505 kb) (Fig. S3). The GC content was lower in holoparasites (mean: 34.93%) than in those of hemiparasites (38.25% on average) and autotrophs (mean: 37.90%). Autotrophs contained all intact genes; the number of intact genes was lower in hemiparasites than in autotrophs, and this decrease primarily stemmed from the pseudogenization/loss of ndh genes (Fig. 2; Table S2). Moreover, non-functionalization and gene loss were observed in most photosynthetic genes (e.g., psa /psb ,ycf 3/4, ndh , and cem A) in holoparasites.