Fig 1.
Chloroplast genome maps of A. gmelinii, A. capillaris, and A. fukudo.
Genes represented on the outside of the outer circle are transcribed clockwise, and those shown on the inside of the outer circle are transcribed counterclockwise. Genes belonging to the same functional group were indicated in the same color. The inner tracks represent inter- and intraspecific variations. Track A and B are intraspecific variations of A. gmelinii and A. capililaris, respectively. Track C and D indicate total SNPs and InDels among five Artemisia chloroplast genomes, respectively.
Fig 2.
A phylogenetic tree of 18 species belonging to the Asteraceae family.
A total of 64 coding regions in the chloroplast genome were used to analyze phylogenetic relationships among the species. The phylogenetic tree was constructed by the neighbor-joining method with 1000 bootstrap values. Numbers on each node were bootstrap values. The accession number of the chloroplast genomes used for the phylogenetic tree are in parenthesis and S2 Table.
Table 1.
Summary of the NGS data and chloroplast genomes of A. gmelinii, A. capillaris, and A. fukudo.
Fig 3.
Chloroplast sequence variation between A. gmelinii, A. capillaris, A. fukudo, and A. frigida.
The molecular markers were developed from the highly variable regions indicated by a red rectangle. The names of markers are shown above the red boxes.
Table 2.
The number of SNPs and InDels found in chloroplast genomes of three Artemisia species.
Fig 4.
Discrimination success for A. gmelinii, A. capillaris, and A. fukudo using InDel-based barcode markers.
Rectangles and dashed lines indicate the genes and intergenic regions, respectively. Arrows represent the inserted sequences within the intergenic regions. The amplified DNA fragments using the InDel-based barcode markers were separated on an agarose gel as shown on the right side (AG, A. gmelinii; AC, A. capillaris; AF, A. fukudo). The detailed sequence variations between the species are presented in S1 Fig.
Fig 5.
Representative LC-MS base peak ion (BPI) chromatograms of the Artemisia extracts.
Tentatively annotated chromatographic peaks are annotated with peak numbers. Gaps between the chromatograms were added to help visualize the differences, so the y-axis values do not equal the absolute intensities.
Table 3.
Chromatographic and spectrometric data of the 28 tentatively identified metabolites from Artemisia species.
Fig 6.
(A) The PCA biplot of the Artemisia samples represented by group marks (Af: A. fukudo; Ag-A: A. gmelinii-A; Ag-B: A. gmelinii-B; Ac-A: A. capillaris-A; Ac-B: A. capillaris-B). The numbers denote PCA loadings of each MS feature. Important marker MS features are labeled with their annotation and peak numbers enlisted in Table 3. Most MS features shown here are [M−H]− ions, but MS features 9 and 372 are in-source fragments of peaks 6 and 23, respectively. (B) Bar plots showing the ion intensities of selected marker peaks (5, 7, 12, 16, and 23) in analyzed Artemisia samples (**** p < 0.0001).