Figure 1.
Map of the chloroplast genome of Dendrobium officinale.
Thick lines indicate inverted repeats (IRs). Genes shown inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise.
Figure 2.
Map of the chloroplast genome of Cypripedium macranthos.
Thick lines indicate inverted repeats (IRs). Genes shown inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise.
Figure 3.
Phylogenomic tree based on 63 protein-coding genes.
Only the BI tree is shown because BI and ML trees had identical topologies. Numbers near branches are posterior probabilities for BI analysis and bootstrap values for ML analysis. The degenerate ndh genes are mapped in the tree. Solid, empty, and gray bars show the distribution of ndh genes in orchids, indicating intact, lost, and pseudogenized genes, respectively.
Table 1.
Comparison of major features of seven orchid chloroplast genomes.
Figure 4.
Comparison of the regions flanking the junctions (JLB, JLA, JSB, and JSA) among seven orchid chloroplast genomes.
Four types of junctions are present at the JSB in seven orchid species. Numbers in green indicate the length of Ψrpl22. Numbers in orange indicate the distance between ndhF and JSB. Numbers in purple indicate the distance between 5′- ycf1 and JSA. Numbers in blue indicate the distance between rps19 and JLA. This figure is not to scale.
Table 2.
Pairwise distances of nucleotide and protein substitutions among six orchid species.
Figure 5.
Phylogenetic tree of the Epidendroideae reconstructed based on combined genes.
BI and ML analyses yielded identical topologies. Posterior probability and bootstrap proportion are indicated near the nodes. Subfamilies, tribes, and subtribes (sensu Chase et al. [2]) are indicated where applicable.