Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua

The complete chloroplast genome of <i>Artemisia annua</i> (Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The <i>A. annua</i> cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the <i>A. annua</i> cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of <i>A. annua</i> is inverted; this fact is consistent with the sequences of chloroplast genomes from three other <i>Artemisia</i> species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In <i>A. annua</i> cpDNA, the <i>rps19</i> gene was found in the LSC region rather than the IR region, and the <i>rps19</i> pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between <i>A. annua</i> and <i>A. fukudo</i> were very slight. A phylogenetic analysis revealed a sister relationship between <i>A. annua</i> and <i>A. fukudo</i>. This study identified the unique characteristics of the <i>A. annua</i> cp genome. These results offer valuable information for future research on <i>Artemisia</i> species identification and for the selective breeding of <i>A. annua</i> with high pharmaceutical efficacy.