Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858–151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

中文翻译：

---

东亚蒿属（菊科）叶绿体基因组比较分析：深入了解进化分歧和系统发育影响。


东亚的艾蒿包括许多重要的经济类群，广泛用于食品、药用和观赏目的。然而，由于诊断形态特征不足和频繁的自然杂交，类群的鉴定受到了阻碍。开发具有足够分辨率的新型 DNA 标记或条形码来解决东亚蒿的分类问题是一项重大挑战。为了建立青蒿分类学鉴定和比较系统发育分析的分子基础，我们新确定了东亚18个青蒿类群的19个叶绿体基因组（质体组）序列，并使用公开的Illumina读数从头组装和注释了两个类群的质体组，并将它们与之前报道的 11 种蒿质体进行比较。蒿质体长度为 150,858–151,318 个碱基对 (bp)，并以保守的顺序和方向包含 87 个蛋白质编码基因、37 个转移 RNA 和 8 个核糖体 RNA 基因。对整个质体和 80 个非冗余蛋白质编码基因的进化分析表明，非编码 trnH-psbA 间隔区在类群之间和内部的大小和核苷酸序列上高度可变，而 accD 和 ycf1 的编码序列处于弱正选择和分别放宽选择性约束。基于最大似然和贝叶斯推理分析的全质体系统发育分析得出了五类蒿质体，聚集在单系龙线亚属和并系蒿亚属中，表明整个质体可以作为分子标记来推断蒿类群的叶绿体单倍型。 此外，对 accD 和 ycf1 热点的分析使得能够开发出可能适用于菊科且具有高辨别力的新型标记。蒿质体的完整序列具有足够的多态性，可以用作该属的超级条形码。它将促进新分子标记的开发和菊科蒿属植物系统发育关系的研究。