Fig 1.
Circular gene map of the I. rubescens chloroplast genome.
Genes inside the circle are transcribed clockwise, and those outside are transcribed counter clockwise. Groups of genes with different functions are color-coded. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content.
Table 1.
List of genes in the chloroplast genome of I. rubescens.
Table 2.
Codon-anticodon recognition patterns and codon usage in the chloroplast genome of I. rubescens.
Table 3.
SSRs in the chloroplast genome of I. rubescens.
Table 4.
Long repeat sequences identified in the chloroplast genome of I. rubescens.
Fig 2.
Sequence alignment of five Isodon chloroplast genomes using mVISTA.
The annotation of I. rubescens (IR-L) was used as the reference. Gray arrows above the alignment indicate the position and direction of transcription of each gene. The scale on the vertical axes represents the percent sequence identity between 50% and 100%. IR-J, IR-X, and IR-L are the three accessions of I. rubescens.
Fig 3.
Sliding window analysis of five complete Isodon chloroplast genomes.
Window length: 800 bp; step size: 200 bp. X-axis: nucleotide positions in the chloroplast genomes. Y-axis: K values of nucleotide diversity. A: I. rubescens from Lushan, Henan province (IR-L), B: I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), C: I. rubescens (MW376483.1) from Jiyuan, Henan Province (IR-J), D: I. serra (MT317099.1), E: I. lophanthoides (MT317098.1). Total: the total nucleotide diversity values for the A vs. B, A vs. C, A vs. D, and A vs. E comparisons.
Fig 4.
Comparison of the LSC, SSC, and IR border regions among the five Isodon chloroplast genomes of examined in this study.
IR-J, IR-X, and IR-L are the three accessions of I. rubescens.
Fig 5.
Phylogenetic tree based on the complete chloroplast genomes from 25 species constructed using the maximum likelihood method.
The Scutellaria baicalensis cpDNA sequence was used as the outgroup. Bootstrap values are shown at the nodes.