Comparative analysis of Artemisia plastomes and insights into the infra-generic phylogenetic relationships of the genus

Abstract Background The genus Artemisia is a taxonomically difficult group comprising 400–500 species mainly distributed in northern hemisphere. Only a limited number of Artemisia plastomes are currently available. Their structure has not been comparatively analyzed, and the phylogenetic backbone of Artemisia based on plastome-scale data has not been reported with dense taxon sampling. This situation has greatly hindered our understanding on the plastome variation patterns and infra-generic relationships of the genus. With the advancement of next generation sequencing technologies, it is becoming easier to obtain and comparatively analyze the plastome, and use it to construct phylogeny. Results In this study, we newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combing with 38 previously published plastomes, a total of 72 complete Artemisia plastomes were comparatively analyzed. The results indicated that the Artemisia plastomes were conserved in terms of structure, GC content, gene number and order. All plastomes have a typical quadripartite structure, comprising 87 protein coding, 37 tRNA, and 8 rRNA genes. The IR regions are similar in length and structure among the compared plastomes, with the generic regions more conserved than intergenic spacer regions. The sequence divergence is higher in LSC and SSC regions than in 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 found to be highly diverse, and could be chosen as candidates of DNA barcode. Phylogenetic relationships constructed using protein coding genes of plastomes were divided into several clades that did not match with previous infra-generic divisions of Artemisia, and four subgenera were not monophyletic. Furthermore, they were also inconsistent with those based on nuclear markers. And the phylogenetic position of A. stracheyi is still controversial. Conslusions This study reveals that the Artemisia plastomes are conservative, especially in structure, gene number and order. Phylogenetic relationships constructed using CDS further confirmed the infra-generic divisions of Artemisia were not natural. This study lay a foundation for future evolutionary studies of Artemisia.