Comparative Analysis of Artemisia Plastomes, with Implications for Revealing Phylogenetic Incongruence and Evidence of Hybridization

<b>Background</b>: With the advancement of the next-generation sequencing technology, it is becoming more cost-effective to obtain plastomes from genome skimming data at shallow sequencing depth. <i>Artemisia</i> is a species-rich genus, comprising species of great medicinal or economic value. However, plastomes of <i>Artemisia</i> have not been thoroughly and comparatively analyzed, and the phylogenetic relationships within the genus are still not well resolved. <b>Methods</b>: In this study, 19 <i>Artemisia</i> plastomes were obtained from genome skimming data. Together with the plastomes retrieved from the public database, comparative analyses of their structure were also conducted. We further used sequences of plastomes and nuclear internal transcribed spacer sequences to conduct phylogenetic reconstruction. <b>Results</b>: The <i>Artemisia</i> plastomes are conserved in terms of structure, GC content, gene number, and order. Some regions, i.e., <i>accD</i>, <i>ccsA</i>, <i>ndhE</i>, <i>ycf1</i>, <i>ccsA-ndhD</i>, <i>trnG^GCC-trnfM^CAU</i>, were found to be variable and could be chosen as candidates for the DNA barcode. Phylogenetic analyses also confirmed that the four subgenera of <i>Artemisia</i> are not monophyletic. The incongruence between plastid and nuclear phylogenies indicated that hybridization events have occurred during the evolution of the genus. <b>Conclusions</b>: Reconstructed phylogenies using plastome sequences and nuclear internal transcribed spacers improved our understanding of the phylogenetic backbone of <i>Artemisia</i>. In the future, more taxa of <i>Artemisia</i> should be sequenced and analyzed to clarify the evolutionary history.