Table 1.
Characterization of V. fauriei and V. dageletiana chloroplast genomes.
Fig 1.
The circular chloroplast genome maps of V. fauriei and V. dageletiana.
Genes inside the circle are clockwise, and genes outside the circle are counterclockwise. The dark gray graph inside the circle shows GC%. The thick lines in the large circle represent the two inverted repeat (IR) regions dividing the large single-copy (LSC) and small single-copy (SSC) regions. Label intron-containing genes with asterisks.
Fig 2.
Repeat sequence analysis of V. fauriei and V. dageletiana.
(a) Number of single sequence repeats (SSRs) in exons, introns, and intergenic spacers (IGSs). (b) Number of SSRs present in large single-copy (LSC) and small single-copy (SSC), and inverted repeat (IR) regions. (c) Frequency of the four different SSR types. (d) Number of tandem repeats present in exons, introns, and IGSs. (e) Distribution according to the length of tandem repeats. (f) Frequency of different repeat types in the chloroplast genome.
Fig 3.
Comparison of the chloroplast genomes of three Valeriana species using mVISTA.
Regions where sequence variation exists between chloroplast genomes are shown in white, and identity is indicated in the 50–100% range. Gray arrows above the alignment indicate the forward and reverse orientation of genes. The purple bars represent exons, and the pink bars represent conserved non-coding sequences. The yellow mark below the bar indicates the inverted repeat regions (IRs).
Fig 4.
Comparison of the three Valeriana species’ nucleotide diversity (Pi) values.
The light gray background indicates a large single-copy (LSC) region, gray indicates an inverted repeat (IR) region, and dark gray indicates a small single-copy (SSC) region. The top six values in the data are indicated numerically in the figure.
Fig 5.
dN/dS ratios of chloroplast protein-coding genes across Valeriana species.
(a) Heatmap illustrating the dN/dS values for 14 selected protein-coding genes in V. fauriei, V. dageletiana, V. officinalis, and V. jatamansi. The color gradient represents dN/dS values, with blue indicating lower ratios and red indicating higher ratios. (b) Bar chart showing the same dN/dS values for these genes across the four species, with different colors representing each species.
Fig 6.
Phylogenetic tree showing the combined Maximum Likelihood (ML) bootstrap and Bayesian Inference (BI) probabilities based on 66 coding sequences (CDSs) of Valeriana, with F. cornucopiae as the closest relative and Dipsacaceae and Scabioseae as the outgroups.
Numbers at the nodes indicate ML bootstrap (left) and BI posterior probabilities (right).
Fig 7.
Divergence time estimates based on a Bayesian tree using 66 protein-coding genes.
Operational taxonomic units (OTUs) represent Valerianeae, Dipsacaceae, and Scabioseae. Numbers along branches denote mean divergence ages (million years ago, MYA), and 95% highest posterior density (HPD) intervals are shown for each node. P: Pliocene; Q: Quaternary (includes the Holocene and Pleistocene).