Background: Artemisia is a large and complex genus comprising about 500 species. Currently, only a limited number of plastomes (the chloroplast genome) of Artemisia are available. Their structures have not been comparatively analyzed, and a phylogenetic backbone based on plastome-scale data is still lacking. This situation has greatly hindered our understanding of the plastome variation patterns and infra-generic relationships of the genus. Methods: We newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combining this with previously published plastomes, we comparatively analyzed their structure and constructed phylogenetic relationships using the protein-coding sequences (CDS) of plastomes. Results: Our analyses indicated that the Artemisia plastomes are conserved in terms of their structure, GC content, gene number, and order. The sequence divergence is higher in the LSC and SSC regions than in the IR regions. Three protein-coding genes and four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), and ndhG-ndhI, were highly diverse and could be chosen as candidates of DNA barcodes. Phylogenetic trees were divided into several clades, and all four main subgenera were not monophyletic. Additionally, the phylogenetic position of A. stracheyi is still controversial. Conclusions: Plastomes can provide important information for phylogenetic constructions. This study provides insights into the infra-generic relationships within Artemisia and also lays a foundation for future evolutionary studies of this genus.

Based on observations on herbarium specimens (including type material) and living plants in the wild, we demonstrate that Artemisia flaccida (Asteraceae, Anthemideae) is conspecific with A. fulgens and that A. flaccida var. meiguensis deserves a varietal status under A. fulgens. We therefore place A. flaccida in synonymy with A. fulgens and transfer A. flaccida var. meiguensis to A. fulgens as A. fulgens var. meiguensis. Lectotypification is proposed for A. fulgens and A. flaccida. The geographical distribution of the two varieties of A. fulgens, var. fulgens and var. meiguensis, is also clarified.

Based on observations on both herbarium specimens (including type material) and living plants in the wild, we demonstrate that the Chinese species Artemisia neosinensis (Asteraceae, Anthemideae) has been strikingly misunderstood by previous authors and its geographical range has been wrongly largely extended. All the non-type specimens cited under this species by them belong to misidentifications, whereas the specimens of true A. neosinensis have been wrongly referred to other species. This species is characterized by having 1-pinnatisect, adaxially tomentose, abaxially arachnoid-tomentose leaves with ovate-acuminate or ovate lobules of segments, and campanulate capitula with abaxially arachnoid-tomentose phyllaries. It is distributed only in western Sichuan and northwestern Yunnan, not in Gansu, Qinghai and Xizang. The syntypes of A. strongylocephala var. sinensis f. virgata, a synonym of A. neosinensis, include two taxa, A. neosinensis and A. tangutica var. tomentosa. Lectotypification is thus proposed for A. strongylocephala var. sinensis f. virgata.

The chromosome numbers of 56 populations belonging to 25 species and 4 varieties of Artemisia L. (Asteraceae) from China were examined, and those of 13 species and four varieties are reported here for the first time. The karyotypes of 39 populations in 23 species and four varieties were also studied. Among them, twelve species and one variety were found to be diploid, with 2n = 16 or 18; nine species and three varieties were found to be tetraploid, with 2n = 32 or 36; and two species were found to have both diploid and tetraploid cytotypes. Two species were found to have aneuploid cytotypes. The karyotypes of Artemisia are similar, with most chromosomes belonging to median-centromeric (m) and a few belonging to submedian-centromeric (sm) or subterminal-centromeric (st). The high level of polyploids in Artemisia from the Qinghai–Tibetan Plateau indicates that polyploidy has played an important role in the evolutionary speciation of this highly diversified genus in this region.

Background: 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. Artemisia is a species-rich genus, comprising species of great medicinal or economic value. However, plastomes of Artemisia have not been thoroughly and comparatively analyzed, and the phylogenetic relationships within the genus are still not well resolved. Methods: In this study, 19 Artemisia 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. Results: The Artemisia plastomes are conserved in terms of structure, GC content, gene number, and order. Some regions, i.e., accD, ccsA, ndhE, ycf1, ccsA-ndhD, trnG^GCC-trnfM^CAU, were found to be variable and could be chosen as candidates for the DNA barcode. Phylogenetic analyses also confirmed that the four subgenera of Artemisia are not monophyletic. The incongruence between plastid and nuclear phylogenies indicated that hybridization events have occurred during the evolution of the genus. Conclusions: Reconstructed phylogenies using plastome sequences and nuclear internal transcribed spacers improved our understanding of the phylogenetic backbone of Artemisia. In the future, more taxa of Artemisia should be sequenced and analyzed to clarify the evolutionary history.