Additional file 1 : Figure S1 to S7. Fig. S1. Comparison of the IR border regions of the Asteraceae plastomes. Fig. S2. Multiple alignments of accD coding sequences in the 32 Artemisia plastomes showing hotspots of nucleotide sequence diversity. Eight positively selected amino acid substitutions are indicated by red triangles. The core hotspot of 276 bp in length (616–963 bp over the gapped alignment) is indicated by arrows. Fig. S3. A ML tree based on the whole plastomes of 32 Artemisia taxa. Bootstrap values are indicated on the nodes. Colored lines and braces at the right of the tree indicate section and subgenus names of Artemisia, respectively, that include taxa. Fig. S4. A ML tree of ycf1 in the Asteraceae family. Taxa belonging to the same supertribe or subfamily are grouped. Fig. S5. A ML tree of accD in the Asteraceae family. Taxa belonging to the same supertribe or subfamily are grouped. Fig. S6. Performances of accD and ycf1 in identifying the Asteraceae taxa using BLAST search. Hits with 100% identity were counted into two categories, unique hit and cross-hit to other species or tribe(s). Fig. S7. A ML tree based on the accD-1 k + ycf1b marker sequences of 32 Artemisia taxa. Bootstrap values are indicated on the nodes.