Figure 1.
The map of the three Camellia chloroplast genome sequences.
Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction. Dashed area in the inner circle indicates the GC content of the chloroplast genome.
Table 1.
Summary of the chloroplast genome sequencing, assembly and features.
Figure 2.
ML phylogram of the angiosperms.
The tree has a –lnL = 938438.26. Numbers at the nodes are ML bootstrap support values. Three Camellia chloroplast genomes reported here are highlighted in bold. The red branches indicate that intact ycf15 gene is present in related species and asterisks on the top right corner of the species indicate putative losses of ycf15 gene. Scale bar indicates the increment of 0.01 substitutions per site.
Figure 3.
Alignment of the ycf15 gene and protein sequences in the ten representative species of angiosperms.
A) alignment of the ycf15 gene sequences; B) alignment of the ycf15 protein sequences. Black asterisks indicate stop codon in protein sequence.
Figure 4.
ML phylogram of 55 taxa based on ycf15 gene sequences.
The analyzed genes include both intact and disabled sequences. The tree has a –lnL = 1983.94. Bootstrap support values >50% are given at nodes. The red branches indicate that intact ycf15 gene is present in related species. Scale bar indicates the increment of 0.01 substitutions per site.
Figure 5.
Circular plot of transcriptome reads mapping of the C. sinensis var. assamica chloroplast genome.
The first ring shows genome structure of C. sinensis var. assamica, while the second and third rings show genes in the Camellia chloroplast genome that transcribed clockwise and counter clockwise, respectively. The next two rings show transcriptome reads from C. sinensis var. assamica and C. sinensis var. sinensis were separately mapped to the genome. Log10 of reads depth for each base was calculated and plotted across the genome. The figure was constructed using Circos [57].
Table 2.
RNA editing detected by transcriptome reads mapping.