Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Abstract

Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.

Comparative analysis of medicinal plant Isodon rubescens and its common adulterants based on chloroplast genome sequencing

“…This phenomenon might be explained by the fact that the geographical area of origin might influence the variation of I. rubescens. Another previous study supported the same conclusion; the Artemisia argyi collected from different geographical areas display high intraspecific diversity in the cp genome (Chen et al, 2022). In addition, clade B only includes a species of I. ternifolious, which was supported by the findings of other researchers based on trnD-trnT, psbA-trnH, rpl32-trnL, trnL-trnF, rps16, and nrITS (Zhong et al, 2010;Yu et al, 2014;Chen et al, 2021).…”

Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis

“…Contraction and expansion of the IR/SC region boundaries are the main reason for changes in chloroplast genome length, playing a vital role in its evolution. These boundaries can be used to study species-specific gene loci (Gui et al 2020), and previous studies found that the IR/LSC and IR/SSC junctions vary among Artemisia species (Chen et al 2022). Here, we found only slight differences in IR boundaries between the nine Artemisia species, indicating these species are closely related.…”

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

“…The cp genomes of five Artemisia species contain 114 genes, which was similar to those of Artemisia annua ( Shen et al., 2017 ). Like most other Artemisia species, ycf1 and rps19 were also detected, but the copy number and location were different, ycf1 spans the IRb/SSC boundary, this was also seen in A. scoparia and A. absinthium ( Chen et al., 2022 ). The GC content of the IR region was significantly greater than that of the LSC and SSC regions.…”

“…species, ycf1 and rps19 were also detected, but the copy number and location were different, ycf1 spans the IRb/SSC boundary, this was also seen in A. scoparia and A. absinthium (Chen et al, 2022). The GC content of the IR region was significantly greater than that of the LSC and SSC regions.…”